* MS:$sequence(7,0,9999999)$ * PEFF:$sequence(7,0,9999999)$ 12:02:2025 17:58 MS 1.2 Eric Deutsch For any queries contact psidev-ms-vocab@lists.sourceforge.net This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics coverage: Mass spectrometer output files and spectra interpretation creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de> creator: Chris Bielow <chris.bielow <-at-> fu-berlin.de> creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org> creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se> creator: Gerhard Mayer <mayerg97 <-at-> rub.de> creator: Joshua Klein <jaklein <-at-> bu.edu> creator: Julian Uszkoreit <julian.uszkoreit <-at-> ruhr-uni-bochum.de> creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de> creator: Mathias Walzer <walzer <-at-> ebi.ac.uk> creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu> creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de> creator: Nithu Sara John <nithu <-at-> ebi.ac.uk> creator: Pierre-Alain Binz <pierre-alain.binz <-at-> chuv.ch> creator: Wout Bittremieux <wout.bittremieux <-at-> uantwerpen.be> creator: Yasset Perez-Riverol <yperez <-at-> ebi.ac.uk> namespace: MS namespace: PEFF publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group definition term replaced by namespace-id-rule created by creation date has_alternative_id database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym id in_subset shorthand BFO:0000050 MS part_of part_of part_of MS has_column has_column MS has_domain has_domain MS has_metric_category has_metric_category MS has_optional_column has_optional_column MS has_order has_order MS has_regexp has regexp The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format. MS has_structured_representation_in_format has structured representation in format MS has_units has_units MS has_value_concept has_value_concept 'Entity A' has value type 'Entity B', such as xsd:float. MS has_value_type has value type Proteomics Standards Initiative Mass Spectrometry Vocabularies. MS MS:0000000 Proteomics Standards Initiative Mass Spectrometry Vocabularies Proteomics Standards Initiative Mass Spectrometry Vocabularies. PSI:MS A reference number relevant to the sample under study. MS MS:1000001 sample number A reference number relevant to the sample under study. PSI:MS A reference string relevant to the sample under study. MS MS:1000002 sample name A reference string relevant to the sample under study. PSI:MS The chemical phase of a pure sample, or the state of a mixed sample. MS MS:1000003 sample state The chemical phase of a pure sample, or the state of a mixed sample. PSI:MS Total mass of sample used. MS MS:1000004 sample mass Total mass of sample used. PSI:MS Total volume of solution used. MS MS:1000005 sample volume Total volume of solution used. PSI:MS Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used. MS MS:1000006 sample concentration Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used. PSI:MS The nature of the sample inlet. MS MS:1000007 inlet type The nature of the sample inlet. PSI:MS The method by which gas phase ions are generated from the sample. MS MS:1000008 ionization type The method by which gas phase ions are generated from the sample. PSI:MS OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer. MS MS:1000009 This term was made obsolete because it was replaced by scan polarity (MS:1000465). ionization mode true OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer. PSI:MS OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted. MS MS:1000010 This former purgatory term was made obsolete. analyzer type true OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted. PSI:MS Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height. MS MS:1000011 mass resolution Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height. PSI:MS Which of the available standard measures is used to define whether two peaks are separate. MS MS:1000012 resolution measurement method Which of the available standard measures is used to define whether two peaks are separate. PSI:MS OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z. MS MS:1000013 This former purgatory term was made obsolete. resolution type true OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z. PSI:MS Accuracy is the degree of conformity of a measured mass to its actual value. MS MS:1000014 accuracy Accuracy is the degree of conformity of a measured mass to its actual value. PSI:MS Rate in Th/sec for scanning analyzers. MS MS:1000015 scan rate Rate in Th/sec for scanning analyzers. PSI:MS The time that an analyzer started a scan, relative to the start of the MS run. MS MS:1000016 scan start time The time that an analyzer started a scan, relative to the start of the MS run. PSI:MS OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum. MS MS:1000017 OBSOLETE This former purgatory term was made obsolete. Scan Function true OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum. PSI:MS Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low). MS MS:1000018 scan direction Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low). PSI:MS Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used. MS MS:1000019 scan law Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used. PSI:MS Describes the acquisition data type produced by a tandem mass spectrometry experiment. MS Tandem Scanning Method MS:1000020 OBSOLETE This former purgatory term was made obsolete. scanning method true Describes the acquisition data type produced by a tandem mass spectrometry experiment. PSI:MS Status of the reflectron, turned on or off. MS MS:1000021 reflectron state Status of the reflectron, turned on or off. PSI:MS The length of the field free drift space in a time of flight mass spectrometer. MS MS:1000022 TOF Total Path Length The length of the field free drift space in a time of flight mass spectrometer. PSI:MS OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion. MS MS:1000023 This former purgatory term was made obsolete. isolation width true OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion. PSI:MS Final MS level achieved when performing PFF with the ion trap (e.g. MS E10). MS MS:1000024 final MS exponent Final MS level achieved when performing PFF with the ion trap (e.g. MS E10). PSI:MS A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity. B MS Magnetic Field MS:1000025 magnetic field strength A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity. PSI:MS Type of detector used in the mass spectrometer. MS MS:1000026 detector type Type of detector used in the mass spectrometer. PSI:MS Method by which detector signal is acquired by the data system. MS MS:1000027 detector acquisition mode Method by which detector signal is acquired by the data system. PSI:MS The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height. MS MS:1000028 detector resolution The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height. PSI:MS The rate of signal sampling (measurement) with respect to time. ADC Sampling Frequency MS MS:1000029 sampling frequency The rate of signal sampling (measurement) with respect to time. PSI:MS OBSOLETE Name of instrument vendor. MS MS:1000030 This term was made obsolete because it was replaced by instrument model (MS:1000031). vendor true OBSOLETE Name of instrument vendor. PSI:MS Instrument model name not including the vendor's name. MS MS:1000031 instrument model Instrument model name not including the vendor's name. PSI:MS Free text description of a single customization made to the instrument; for several modifications, use several entries. MS MS:1000032 customization Free text description of a single customization made to the instrument; for several modifications, use several entries. PSI:MS The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution. MS MS:1000033 deisotoping The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution. PSI:MS The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions. MS MS:1000034 charge deconvolution The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions. PSI:MS Spectral peak processing conducted on the acquired data to convert profile data to centroided data. MS MS:1000035 peak picking Spectral peak processing conducted on the acquired data to convert profile data to centroided data. PSI:MS OBSOLETE. MS MS:1000036 This term was made obsolete because . scan mode true OBSOLETE. PSI:MS OBSOLETE Terms to describe the polarity setting of the instrument. MS MS:1000037 This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186). polarity true OBSOLETE Terms to describe the polarity setting of the instrument. PSI:MS OBSOLETE Acquisition time in minutes. MS MS:1000038 This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031). minute true OBSOLETE Acquisition time in minutes. PSI:MS OBSOLETE Acquisition time in seconds. MS MS:1000039 This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010). second true OBSOLETE Acquisition time in seconds. PSI:MS Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated. Th mass-to-charge ratio thomson MS MS:1000040 m/z Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated. PSI:MS Number of net charges, positive or negative, on an ion. z MS MS:1000041 charge state Number of net charges, positive or negative, on an ion. PSI:MS Intensity of ions as measured by the height or area of a peak in a mass spectrum. MS MS:1000042 peak intensity Intensity of ions as measured by the height or area of a peak in a mass spectrum. PSI:MS Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors. MS MS:1000043 intensity unit Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors. PSI:MS Fragmentation method used for dissociation or fragmentation. MS Activation Method MS:1000044 dissociation method Fragmentation method used for dissociation or fragmentation. PSI:MS Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. MS MS:1000045 collision energy Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. PSI:MS OBSOLETE Energy units are represented in either eV or Joules. MS MS:1000046 This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111). energy unit true OBSOLETE Energy units are represented in either eV or Joules. PSI:MS State if the sample is in emulsion form. MS MS:1000047 emulsion State if the sample is in emulsion form. PSI:MS State if the sample is in gaseous form. MS MS:1000048 gaseous sample state State if the sample is in gaseous form. PSI:MS State if the sample is in liquid form. MS MS:1000049 liquid sample state State if the sample is in liquid form. PSI:MS State if the sample is in solid form. MS MS:1000050 solid sample state State if the sample is in solid form. PSI:MS State if the sample is in solution form. MS MS:1000051 solution State if the sample is in solution form. PSI:MS State if the sample is in suspension form. MS MS:1000052 suspension State if the sample is in suspension form. PSI:MS Sample batch lot identifier. MS MS:1000053 sample batch Sample batch lot identifier. PSI:MS OBSOLETE Chromatographic conditions used to obtain the sample. MS MS:1000054 This former purgatory term was made obsolete. chromatography true OBSOLETE Chromatographic conditions used to obtain the sample. PSI:MS Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix. CF-FAB MS MS:1000055 continuous flow fast atom bombardment Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix. PSI:MS The sample is directly inserted into the ion source, usually on the end of a heatable probe. MS MS:1000056 direct inlet The sample is directly inserted into the ion source, usually on the end of a heatable probe. PSI:MS Inlet used for introducing the liquid sample into an electrospray ionization source. MS MS:1000057 electrospray inlet Inlet used for introducing the liquid sample into an electrospray ionization source. PSI:MS Sample is directly injected or infused into the ionization source. MS MS:1000058 flow injection analysis Sample is directly injected or infused into the ionization source. PSI:MS A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction. MS MS:1000059 inductively coupled plasma A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction. PSI:MS The continuous flow of solution of a sample into the ionization source. MS MS:1000060 infusion The continuous flow of solution of a sample into the ionization source. PSI:MS A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity. MS MS:1000061 jet separator A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity. PSI:MS A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane. MS MS:1000062 membrane separator A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane. PSI:MS Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules. MS MS:1000063 moving belt Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules. PSI:MS Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules. MS MS:1000064 moving wire Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules. PSI:MS A division of flowing stream of liquid into two streams. MS MS:1000065 open split A division of flowing stream of liquid into two streams. PSI:MS Method for generating ions from a solution of an analyte. MS MS:1000066 particle beam Method for generating ions from a solution of an analyte. PSI:MS A sample inlet method involving a reservoir. MS MS:1000067 reservoir A sample inlet method involving a reservoir. PSI:MS A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber. MS MS:1000068 septum A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber. PSI:MS A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample. MS MS:1000069 thermospray inlet A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample. PSI:MS Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization. APCI MS MS:1000070 atmospheric pressure chemical ionization Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization. PSI:MS The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization. CI MS MS:1000071 chemical ionization The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization. PSI:MS OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. EI MS MS:1000072 This term was made obsolete because it was replaced by electron ionization (MS:1000389). Electronic Ionization true OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. PSI:MS A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended. ESI MS MS:1000073 electrospray ionization A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended. PSI:MS The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization. FAB MS MS:1000074 fast atom bombardment ionization The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization. PSI:MS The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization. MALDI MS MS:1000075 matrix-assisted laser desorption ionization The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization. PSI:MS OBSOLETE. MS MS:1000076 This term was made obsolete because it was replaced by negative scan (MS:1000129). negative ion mode true OBSOLETE. PSI:MS OBSOLETE. MS MS:1000077 This term was made obsolete because it was replaced by positive scan (MS:1000130). positive ion mode true OBSOLETE. PSI:MS A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer. MS MS:1000078 axial ejection linear ion trap A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer. PSI:MS A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z. FT_ICR MS MS:1000079 fourier transform ion cyclotron resonance mass spectrometer A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z. PSI:MS A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z. MS MS:1000080 magnetic sector A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z. PSI:MS A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. MS MS:1000081 quadrupole A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. PSI:MS Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials. Paul Ion trap QIT Quistor MS MS:1000082 quadrupole ion trap Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials. PSI:MS A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer. MS MS:1000083 radial ejection linear ion trap A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer. PSI:MS Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy. TOF MS MS:1000084 time-of-flight Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy. PSI:MS An attribute of resolution when recording the detector response in absence of the analyte. MS MS:1000085 baseline An attribute of resolution when recording the detector response in absence of the analyte. PSI:MS A measure of resolution represented as width of the peak at half peak height. FWHM MS MS:1000086 full width at half-maximum A measure of resolution represented as width of the peak at half peak height. PSI:MS An attribute of resolution when the ratio between adjacent signals is 10% of the signal height. MS MS:1000087 ten percent valley An attribute of resolution when the ratio between adjacent signals is 10% of the signal height. PSI:MS OBSOLETE When resolution is constant with respect to m/z. MS MS:1000088 This child of the former purgatory term resolution type was made obsolete. constant true OBSOLETE When resolution is constant with respect to m/z. PSI:MS OBSOLETE When resolution is proportional with respect to m/z. MS MS:1000089 This child of the former purgatory term resolution type was made obsolete. proportional true OBSOLETE When resolution is proportional with respect to m/z. PSI:MS OBSOLETE A variation of instrument where a selected mass is scanned. MS MS:1000090 This child of the former purgatory term Scan Function was made obsolete. mass scan true OBSOLETE A variation of instrument where a selected mass is scanned. PSI:MS OBSOLETE Please see Single Ion Monitoring. MS MS:1000091 This child of the former purgatory term Scan Function was made obsolete. selected ion detection true OBSOLETE Please see Single Ion Monitoring. PSI:MS High to low direction in terms of m/z of the scan for scanning analyzers. MS MS:1000092 decreasing m/z scan High to low direction in terms of m/z of the scan for scanning analyzers. PSI:MS Low to high direction in terms of m/z of the scan for scanning analyzers. MS MS:1000093 increasing m/z scan Low to high direction in terms of m/z of the scan for scanning analyzers. PSI:MS The mass scan is done in exponential mode. MS MS:1000094 exponential The mass scan is done in exponential mode. PSI:MS OBSOLETE The mass scan is done in linear mode. MS MS:1000095 This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199). linear true OBSOLETE The mass scan is done in linear mode. PSI:MS The mass scan is done in quadratic mode. MS MS:1000096 quadratic The mass scan is done in quadratic mode. PSI:MS OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. MS MS:1000097 This former purgatory term was made obsolete. constant neutral mass loss true OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. PSI:MS OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring. MS MS:1000098 This former purgatory term was made obsolete. multiple ion monitoring true OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring. PSI:MS OBSOLETE This term is not recommended. See Selected Reaction Monitoring. MRM MS MS:1000099 This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206). multiple reaction monitoring true OBSOLETE This term is not recommended. See Selected Reaction Monitoring. PSI:MS OBSOLETE The specific scan function or process that will record a precursor ion spectrum. MS MS:1000100 This former purgatory term was made obsolete. precursor ion scan true OBSOLETE The specific scan function or process that will record a precursor ion spectrum. PSI:MS OBSOLETE The specific scan function or process that records product ion spectrum. MS MS:1000101 This former purgatory term was made obsolete. product ion scan true OBSOLETE The specific scan function or process that records product ion spectrum. PSI:MS OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum. MS MS:1000102 This term was made obsolete because it was replaced by single ion monitoring (MS:100205). single ion monitoring true OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum. PSI:MS OBSOLETE This term is not recommended. See Selected Reaction Monitoring. MS MS:1000103 This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206). single reaction monitoring true OBSOLETE This term is not recommended. See Selected Reaction Monitoring. PSI:MS OBSOLETE None. MS MS:1000104 This term was made obsolete because . None ?? true OBSOLETE None. PSI:MS Reflectron is off. MS MS:1000105 reflectron off Reflectron is off. PSI:MS Reflectron is on. MS MS:1000106 reflectron on Reflectron is on. PSI:MS A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse. Channeltron Detector MS MS:1000107 channeltron A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse. PSI:MS A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected. MS MS:1000108 conversion dynode electron multiplier A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected. PSI:MS A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier. MS ion-to-photon detector MS:1000109 conversion dynode photomultiplier A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier. PSI:MS Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector. Daly MS MS:1000110 daly detector Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector. PSI:MS A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. EMT MS MS:1000111 electron multiplier tube A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. PSI:MS A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device. MS MS:1000112 faraday cup A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device. PSI:MS An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. MS MS:1000113 focal plane array An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. PSI:MS A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate. multichannel plate MS MS:1000114 microchannel plate detector A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate. PSI:MS A detector system commonly used in inductively coupled plasma mass spectrometers. MS MS:1000115 multi-collector A detector system commonly used in inductively coupled plasma mass spectrometers. PSI:MS A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected. PMT MS MS:1000116 photomultiplier A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected. PSI:MS Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers. ADC MS MS:1000117 analog-digital converter Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers. PSI:MS Definition to do. MS MS:1000118 pulse counting Definition to do. PSI:MS A device for converting a signal of sporadic pluses into a digital representation of their time indices. TDC MS MS:1000119 time-digital converter A device for converting a signal of sporadic pluses into a digital representation of their time indices. PSI:MS A detector acquisition mode used for detecting transient signals. MS MS:1000120 transient recorder A detector acquisition mode used for detecting transient signals. PSI:MS The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as "Applied Biosystems|MDS SCIEX". MS Applied Biosystems|MDS SCIEX MS:1000121 SCIEX instrument model The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as "Applied Biosystems|MDS SCIEX". PSI:MS Bruker Daltonics' instrument model. MS MS:1000122 Bruker Daltonics instrument model Bruker Daltonics' instrument model. PSI:MS IonSpec corporation instrument model. MS MS:1000123 IonSpec instrument model IonSpec corporation instrument model. PSI:MS Shimadzu corporation instrument model. MS MS:1000124 Shimadzu instrument model Shimadzu corporation instrument model. PSI:MS ThermoFinnigan from Thermo Electron Corporation instrument model. MS MS:1000125 Thermo Finnigan instrument model ThermoFinnigan from Thermo Electron Corporation instrument model. PSI:MS Waters Corporation instrument model. MS MS:1000126 Waters instrument model Waters Corporation instrument model. PSI:MS Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. Discrete Mass Spectrum MS MS:1000127 centroid spectrum Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. PSI:MS A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. Continuum Mass Spectrum continuous mass spectrum MS MS:1000128 profile spectrum A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. PSI:MS Polarity of the scan is negative. MS MS:1000129 negative scan Polarity of the scan is negative. PSI:MS Polarity of the scan is positive. MS MS:1000130 positive scan Polarity of the scan is positive. PSI:MS The number of counted events observed in one or a group of elements of a detector. MS MS:1000131 number of detector counts The number of counted events observed in one or a group of elements of a detector. PSI:MS The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity. MS MS:1000132 percent of base peak The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity. PSI:MS The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended. CAD CID collisionally activated dissociation MS MS:1000133 collision-induced dissociation The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended. PSI:MS The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. PD MS MS:1000134 plasma desorption The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. PSI:MS A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra. PSD MS MS:1000135 post-source decay A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra. PSI:MS Fragmentation that results from the collision of an ion with a surface. SID MS MS:1000136 surface-induced dissociation Fragmentation that results from the collision of an ion with a surface. PSI:MS OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J. MS MS:1000137 This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266). electron volt true OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J. PSI:MS Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions. MS MS:1000138 normalized collision energy Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions. PSI:PI Applied Biosystems/MDS SCIEX Q 4000 TRAP MS. MS MS:1000139 4000 QTRAP Applied Biosystems/MDS SCIEX Q 4000 TRAP MS. PSI:MS Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS. MS MS:1000140 4700 Proteomics Analyzer Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS. PSI:MS Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. MS MS:1000141 apex IV Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. PSI:MS Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. MS MS:1000142 apex Q Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. PSI:MS Applied Biosystems/MDS SCIEX API 150EX MS. MS MS:1000143 API 150EX Applied Biosystems/MDS SCIEX API 150EX MS. PSI:MS Applied Biosystems/MDS SCIEX API 150EX Prep MS. MS MS:1000144 API 150EX Prep Applied Biosystems/MDS SCIEX API 150EX Prep MS. PSI:MS Applied Biosystems/MDS SCIEX API 2000 MS. MS MS:1000145 API 2000 Applied Biosystems/MDS SCIEX API 2000 MS. PSI:MS Applied Biosystems/MDS SCIEX API 3000 MS. MS MS:1000146 API 3000 Applied Biosystems/MDS SCIEX API 3000 MS. PSI:MS Applied Biosystems/MDS SCIEX API 4000 MS. MS MS:1000147 API 4000 Applied Biosystems/MDS SCIEX API 4000 MS. PSI:MS Bruker Daltonics' autoflex II: MALDI TOF. MS MS:1000148 autoflex II Bruker Daltonics' autoflex II: MALDI TOF. PSI:MS Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF. MS MS:1000149 autoflex TOF/TOF Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF. PSI:MS Waters magnetic sector based AutoSpec Ultima NT MS. MS MS:1000150 Auto Spec Ultima NT Waters magnetic sector based AutoSpec Ultima NT MS. PSI:MS Bruker Daltonics' BioTOF II: ESI TOF. MS MS:1000151 BioTOF II Bruker Daltonics' BioTOF II: ESI TOF. PSI:MS Bruker Daltonics' BioTOF-Q: ESI Q-TOF. MS MS:1000152 BioTOF-Q Bruker Daltonics' BioTOF-Q: ESI Q-TOF. PSI:MS ThermoFinnigan DELTA plusAdvantage MS. MS MS:1000153 DELTA plusAdvantage ThermoFinnigan DELTA plusAdvantage MS. PSI:MS ThermoFinnigan DELTAplusXP MS. MS MS:1000154 DELTAplusXP ThermoFinnigan DELTAplusXP MS. PSI:MS OBSOLETE ThermoFinnigan ELEMENT2 MS. MS MS:1000155 This former purgatory term was made obsolete. ELEMENT2 true OBSOLETE ThermoFinnigan ELEMENT2 MS. PSI:MS Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. MS MS:1000156 esquire 4000 Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. PSI:MS Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. MS MS:1000157 esquire 6000 Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. PSI:MS IonSpec Explorer MS. MS MS:1000158 explorer IonSpec Explorer MS. PSI:MS Waters oa-ToF based GCT. MS MS:1000159 GCT Waters oa-ToF based GCT. PSI:MS Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI. MS MS:1000160 HCT Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI. PSI:MS Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI. MS MS:1000161 HCTplus Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI. PSI:MS IonSpec HiResESI MS. MS MS:1000162 HiRes ESI IonSpec HiResESI MS. PSI:MS IonSpec HiResMALDI MS. MS MS:1000163 HiRes MALDI IonSpec HiResMALDI MS. PSI:MS Waters IsoPrime MS. MS MS:1000164 IsoPrime Waters IsoPrime MS. PSI:MS Waters IsoProbe MS. MS MS:1000165 IsoProbe Waters IsoProbe MS. PSI:MS Waters IsoProbe T MS. MS MS:1000166 IsoProbe T Waters IsoProbe T MS. PSI:MS ThermoFinnigan LCQ Advantage MS. MS MS:1000167 LCQ Advantage ThermoFinnigan LCQ Advantage MS. PSI:MS ThermoFinnigan LCQ Classic MS. MS MS:1000168 LCQ Classic ThermoFinnigan LCQ Classic MS. PSI:MS ThermoFinnigan LCQ Deca XP Plus MS. MS MS:1000169 LCQ Deca XP Plus ThermoFinnigan LCQ Deca XP Plus MS. PSI:MS Waters oa-ToF based MALDI L. MS MS:1000170 M@LDI L Waters oa-ToF based MALDI L. PSI:MS Waters oa-ToF based MALDI LR. MS MS:1000171 M@LDI LR Waters oa-ToF based MALDI LR. PSI:MS ThermoFinnigan MAT253 MS. MS MS:1000172 MAT253 ThermoFinnigan MAT253 MS. PSI:MS ThermoFinnigan MAT900XP MS. MS MS:1000173 MAT900XP ThermoFinnigan MAT900XP MS. PSI:MS ThermoFinnigan MAT900XP Trap MS. MS MS:1000174 MAT900XP Trap ThermoFinnigan MAT900XP Trap MS. PSI:MS ThermoFinnigan MAT95XP MS. MS MS:1000175 MAT95XP ThermoFinnigan MAT95XP MS. PSI:MS ThermoFinnigan MAT95XP Trap MS. MS MS:1000176 MAT95XP Trap ThermoFinnigan MAT95XP Trap MS. PSI:MS Bruker Daltonics' microflex: MALDI TOF. MS MS:1000177 microflex Bruker Daltonics' microflex: MALDI TOF. PSI:MS Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI. MS MS:1000178 microTOF LC Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI. PSI:MS ThermoFinnigan NEPTUNE MS. MS MS:1000179 neptune ThermoFinnigan NEPTUNE MS. PSI:MS Waters NG-5400 MS. MS MS:1000180 NG-5400 Waters NG-5400 MS. PSI:MS IonSpec OMEGA MS. MS MS:1000181 OMEGA IonSpec OMEGA MS. PSI:MS IonSpec OMEGA-2001 MS. MS MS:1000182 OMEGA-2001 IonSpec OMEGA-2001 MS. PSI:MS Bruker Daltonics' OmniFlex: MALDI TOF. MS MS:1000183 OmniFlex Bruker Daltonics' OmniFlex: MALDI TOF. PSI:MS Waters Platform ICP MS. MS MS:1000184 Platform ICP Waters Platform ICP MS. PSI:MS ThermoFinnigan PolarisQ MS. MS MS:1000185 PolarisQ ThermoFinnigan PolarisQ MS. PSI:MS Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS. MS MS:1000186 proteomics solution 1 Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS. PSI:MS Applied Biosystems/MDS SCIEX Q TRAP MS. MS MS:1000187 Q TRAP Applied Biosystems/MDS SCIEX Q TRAP MS. PSI:MS Waters oa-ToF based Q-Tof micro. MS MS:1000188 Q-Tof micro Waters oa-ToF based Q-Tof micro. PSI:MS Waters oa-ToF based Q-Tof Ultima. MS MS:1000189 Q-Tof Ultima Waters oa-ToF based Q-Tof Ultima. PSI:MS Applied Biosystems/MDS SCIEX QSTAR MS. MS MS:1000190 QSTAR Applied Biosystems/MDS SCIEX QSTAR MS. PSI:MS Waters (triple) quadrupole based micro. MS MS:1000191 quattro micro Waters (triple) quadrupole based micro. PSI:MS Waters (triple) quadrupole based Ultima. MS MS:1000192 Quattro Ultima Waters (triple) quadrupole based Ultima. PSI:MS ThermoFinnigan Surveyor MSQ MS. MS MS:1000193 Surveyor MSQ ThermoFinnigan Surveyor MSQ MS. PSI:MS Applied Biosystems/MDS SCIEX SymBiot I MS. MS MS:1000194 SymBiot I Applied Biosystems/MDS SCIEX SymBiot I MS. PSI:MS Applied Biosystems/MDS SCIEX SymBiot XVI MS. MS MS:1000195 SymBiot XVI Applied Biosystems/MDS SCIEX SymBiot XVI MS. PSI:MS ThermoFinnigan TEMPUS TOF MS. MS MS:1000196 TEMPUS TOF ThermoFinnigan TEMPUS TOF MS. PSI:MS ThermoFinnigan TRACE DSQ MS. MS MS:1000197 TRACE DSQ ThermoFinnigan TRACE DSQ MS. PSI:MS ThermoFinnigan TRITON MS. MS MS:1000198 TRITON ThermoFinnigan TRITON MS. PSI:MS ThermoFinnigan TSQ Quantum MS. MS MS:1000199 TSQ Quantum ThermoFinnigan TSQ Quantum MS. PSI:MS IonSpec Ultima MS. MS MS:1000200 ultima IonSpec Ultima MS. PSI:MS Bruker Daltonics' ultraflex: MALDI TOF. MS MS:1000201 ultraflex Bruker Daltonics' ultraflex: MALDI TOF. PSI:MS Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF. MS MS:1000202 ultraflex TOF/TOF Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF. PSI:MS Applied Biosystems/MDS SCIEX Voyager-DE PRO MS. MS MS:1000203 Voyager-DE PRO Applied Biosystems/MDS SCIEX Voyager-DE PRO MS. PSI:MS Applied Biosystems/MDS SCIEX Voyager-DE STR MS. MS MS:1000204 Voyager-DE STR Applied Biosystems/MDS SCIEX Voyager-DE STR MS. PSI:MS The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum. Multiple Ion Monitoring SIM MS MIM MS:1000205 selected ion monitoring The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum. PSI:MS Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space. SRM MS MRM Multiple Reaction Monitoring MS:1000206 selected reaction monitoring Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space. PSI:MS OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition. MS MS:1000207 This child of the former purgatory term ion attribute was made obsolete. accurate mass true OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition. PSI:MS OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance. MS MS:1000208 This child of the former purgatory term ion attribute was made obsolete. average mass true OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance. PSI:MS OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended. AE MS MS:1000209 This child of the former purgatory term ion attribute was made obsolete. appearance energy true OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended. PSI:MS The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures. BP MS MS:1000210 base peak The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures. PSI:MS OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state. MS MS:1000211 OBSOLETE charge number true OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state. PSI:MS OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg. MS MS:1000212 This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221). dalton true OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg. PSI:MS OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy. EA MS MS:1000213 This child of the former purgatory term ion attribute was made obsolete. electron affinity true OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy. PSI:MS OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization. MS MS:1000214 This former purgatory term was made obsolete. electron energy obsolete true OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization. PSI:MS OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom. MS MS:1000215 This child of the former purgatory term ion attribute was made obsolete. exact mass true OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom. PSI:MS A section of a mass spectrometer in which there are no electric or magnetic fields. FFR MS MS:1000216 field-free region A section of a mass spectrometer in which there are no electric or magnetic fields. PSI:MS OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule. MS MS:1000217 This child of the former purgatory term ion reaction was made obsolete. ionization cross section true OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule. PSI:MS OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used. MS MS:1000218 This term was made obsolete because it was replaced by ionization efficiency (MS:1000392). ionization efficiency true OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used. PSI:MS OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion. IE MS MS:1000219 This child of the former purgatory term ion attribute was made obsolete. ionization energy true OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion. PSI:MS OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard. IDMS MS MS:1000220 This child of the former purgatory term mass spectrometry was made obsolete. isotope dilution mass spectrometry true OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard. PSI:MS The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer. MS MS:1000221 magnetic deflection The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer. PSI:MS OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom. MS MS:1000222 This child of the former purgatory term ion attribute was made obsolete. mass defect true OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom. PSI:MS OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion. MS MS:1000223 This child of the former purgatory term ion attribute was made obsolete. mass number true OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion. PSI:MS Mass of a molecule measured in unified atomic mass units (u or Da). MS MS:1000224 molecular mass Mass of a molecule measured in unified atomic mass units (u or Da). https://en.wikipedia.org/wiki/Molecular_mass OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element. MS MS:1000225 This child of the former purgatory term ion attribute was made obsolete. monoisotopic mass true OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element. PSI:MS OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam. MBMS MS MS:1000226 This child of the former purgatory term mass spectrometer was made obsolete. molecular beam mass spectrometry true OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam. PSI:MS Photoionization of an atom or molecule in which in two or more photons are absorbed. MPI MS MS:1000227 multiphoton ionization Photoionization of an atom or molecule in which in two or more photons are absorbed. PSI:MS OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms. MS MS:1000228 This child of the former purgatory term ion reaction was made obsolete. nitrogen rule true OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms. PSI:MS OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value. MS MS:1000229 This child of the former purgatory term ion attribute was made obsolete. nominal mass true OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value. PSI:MS OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions. MS MS:1000230 This child of the former purgatory term ion reaction was made obsolete. odd-electron rule true OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions. PSI:MS A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably. MS MS:1000231 peak A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably. PSI:MS OBSOLETE The height or area of a peak in a mass spectrum. MS MS:1000232 This term was made obsolete because it was replaced by base peak intensity (MS:1000505). peak intensity true OBSOLETE The height or area of a peak in a mass spectrum. PSI:MS OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states. PA MS MS:1000233 This child of the former purgatory term ion attribute was made obsolete. proton affinity true OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states. PSI:MS PA PSI:MS OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported. MS MS:1000234 This term was made obsolete because it was replaced by mass resolving power (MS:1000800). mass resolving power true OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported. PSI:MS Representation of the total ion current detected in each of a series of mass spectra versus time. TIC chromatogram MS MS:1000235 total ion current chromatogram Representation of the total ion current detected in each of a series of mass spectra versus time. PSI:MS The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region. MS MS:1000236 transmission The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region. PSI:MS OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg. u MS MS:1000237 This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221). unified atomic mass unit true OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg. PSI:MS OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy. AMS MS MS:1000238 This child of the former purgatory term mass spectrometer was made obsolete. accelerator mass spectrometry true OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy. PSI:MS Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer. AP MALDI MS MS:1000239 atmospheric pressure matrix-assisted laser desorption ionization Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer. PSI:MS Any ionization process in which ions are formed in the gas phase at atmospheric pressure. API MS MS:1000240 atmospheric pressure ionization Any ionization process in which ions are formed in the gas phase at atmospheric pressure. PSI:MS OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. APPI MS MS:1000241 This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382). Atmostpheric Pressure Photoionization true OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. PSI:MS A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation. BIRD MS MS:1000242 blackbody infrared radiative dissociation A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation. PSI:MS OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site. CRF MS MS:1000243 This child of the former purgatory term ion reaction was made obsolete. charge-remote fragmentation true OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site. PSI:MS OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. CRM MS MS:1000244 This former purgatory term was made obsolete. consecutive reaction monitoring true OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. PSI:MS The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion. CS MS MS:1000245 charge stripping The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion. PSI:MS The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer. DE MS MS:1000246 delayed extraction The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer. PSI:MS The formation of ions from a solid or liquid material after the rapid vaporization of that sample. DI MS MS:1000247 desorption ionization The formation of ions from a solid or liquid material after the rapid vaporization of that sample. PSI:MS A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization. DIP MS MS:1000248 direct insertion probe A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization. PSI:MS The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization. DLI MS MS:1000249 direct liquid introduction The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization. PSI:MS A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments. ECD MS MS:1000250 electron capture dissociation A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments. PSI:MS OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state. EE MS MS:1000251 This child of the former purgatory term ion chemical type was made obsolete. even-electron ion true OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state. PSI:MS OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion. EIEIO MS MS:1000252 This child of the former purgatory term ion reaction was made obsolete. electron-induced excitation in organics true OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion. PSI:MS A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons. EM MS MS:1000253 electron multiplier A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons. PSI:MS A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time. ESA MS MS:1000254 electrostatic energy analyzer A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time. PSI:MS An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa. FA MS MS:1000255 flowing afterglow An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa. PSI:MS OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion. FAIMS MS MS:1000256 This child of the former purgatory term mass spectrometer was made obsolete. high-field asymmetric waveform ion mobility spectrometry true OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion. PSI:MS The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization. FD MS MS:1000257 field desorption The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization. PSI:MS The removal of electrons from any species by interaction with a high electric field. FI MS MS:1000258 field ionization The removal of electrons from any species by interaction with a high electric field. PSI:MS The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas. GD-MS MS MS:1000259 glow discharge ionization The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas. PSI:MS OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge. IKES MS MS:1000260 This child of the former purgatory term mass spectrometer was made obsolete. ion kinetic energy spectrometry true OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge. PSI:MS OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field. IMS MS MS:1000261 This child of the former purgatory term mass spectrometer was made obsolete. ion mobility spectrometry true OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field. PSI:MS Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons. IRMPD MS MS:1000262 infrared multiphoton dissociation Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons. PSI:MS OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer. IRMS MS MS:1000263 This child of the former purgatory term mass spectrometry was made obsolete. isotope ratio mass spectrometry true OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer. PSI:MS A device for spatially confining ions using electric and magnetic fields alone or in combination. IT MS MS:1000264 ion trap A device for spatially confining ions using electric and magnetic fields alone or in combination. PSI:MS OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction. KERD MS MS:1000265 This child of the former purgatory term ion reaction was made obsolete. kinetic energy release distribution true OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction. PSI:MS OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules. MS:1000393 LD Laser Ionization MERGE MS MS:1000266 This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393). Laser Desorption true OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules. PSI:MS OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process. MIKES MS MS:1000267 This child of the former purgatory term mass spectrometer was made obsolete. mass analyzed ion kinetic energy spectrometry true OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process. PSI:MS OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments. MS MS MS:1000268 This former purgatory term was made obsolete. mass spectrometry true OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments. PSI:MS OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions. MS/MS MS MS:1000269 This child of the former purgatory term mass spectrometer was made obsolete. mass spectrometry/mass spectrometry true OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions. PSI:MS OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions. MSn MS MS:1000270 This child of the former purgatory term m/z Separation Method was made obsolete. multiple stage mass spectrometry true OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions. PSI:MS Chemical ionization that results in the formation of negative ions. NICI MS MS:1000271 Negative Ion chemical ionization Chemical ionization that results in the formation of negative ions. PSI:MS With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species. NRMS MS MS:1000272 neutralization reionization mass spectrometry With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species. PSI:MS The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended. PI MS MS:1000273 photoionization The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended. PSI:MS A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source. PyMS MS MS:1000274 pyrolysis mass spectrometry A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source. PSI:MS A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation. q MS MS:1000275 collision quadrupole A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation. PSI:MS Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species. REMPI MS MS:1000276 resonance enhanced multiphoton ionization Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species. PSI:MS OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber. RGA MS MS:1000277 This child of the former purgatory term mass spectrometer was made obsolete. residual gas analyzer true OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber. PSI:MS The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization. SELDI MS MS:1000278 surface enhanced laser desorption ionization The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization. PSI:MS Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface. SEND MS MS:1000279 surface enhanced neat desorption Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface. PSI:MS OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. SI MS MS:1000280 This term was made obsolete because it was replaced by surface ionization (MS:1000406). suface ionization true OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. PSI:MS A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions. SIFT MS MS:1000281 selected ion flow tube A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions. PSI:MS A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time. SORI MS MS:1000282 sustained off-resonance irradiation A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time. PSI:MS OBSOLETE Mass spectrometry using spark ionization. SSMS MS MS:1000283 This term was made obsolete because it was replaced by spark ionization (MS:1000404). Spark Source Mass Spectrometry true OBSOLETE Mass spectrometry using spark ionization. PSI:MS A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments. SWIFT MS MS:1000284 stored waveform inverse fourier transform A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments. PSI:MS The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum. TIC MS MS:1000285 total ion current The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum. PSI:MS Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse. TLF MS MS:1000286 time lag focusing Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse. PSI:MS OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy. TOF-MS MS MS:1000287 This child of the former purgatory term mass spectrometer was made obsolete. time-of-flight mass spectrometer true OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy. PSI:MS A device that uses an oscillating electric field and magnetic field to accelerate charged particles. MS MS:1000288 cyclotron A device that uses an oscillating electric field and magnetic field to accelerate charged particles. PSI:MS OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam. MS MS:1000289 This child of the former purgatory term mass spectrometer was made obsolete. double-focusing mass spectrometer true OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam. PSI:MS OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry. MS MS:1000290 This child of the former purgatory term mass spectrometer was made obsolete. hybrid mass spectrometer true OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry. PSI:MS A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap. MS MS:1000291 linear ion trap A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap. PSI:MS OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate. MS MS:1000292 This former purgatory term was made obsolete. mass spectrograph obsolete true OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate. PSI:MS OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions. MS MS:1000293 This former purgatory term was made obsolete. mass spectrometer true OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions. PSI:MS A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z). MS MS:1000294 mass spectrum A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z). PSI:MS OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians. MS MS:1000295 This former purgatory term was made obsolete. mattauch-herzog geometry true OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians. PSI:MS OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians. MS MS:1000296 This former purgatory term was made obsolete. nier-johnson geometry true OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians. PSI:MS OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected. MS quadrupole ion trap MS:1000297 This term was made obsolete because it is redundant to quadrupole ion trap. paul ion trap true OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected. PSI:MS OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path. MS MS:1000298 This child of the former purgatory term mass spectrometer was made obsolete. prolate traochoidal mass spectrometer true OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path. PSI:MS OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term. MS MS:1000299 This former purgatory term was made obsolete. quistor true OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term. PSI:MS A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time. MS MS:1000300 reflectron A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time. PSI:MS OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection. MS MS:1000301 This child of the former purgatory term mass spectrometer was made obsolete. sector mass spectrometer true OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection. PSI:MS OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry. MS MS:1000302 This child of the former purgatory term mass spectrometer was made obsolete. tandem mass spectrometer true OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry. PSI:MS OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. MS MS:1000303 This child of the former purgatory term mass spectrometer was made obsolete. transmission quadrupole mass spectrometer true OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. PSI:MS The electrical potential used to impart kinetic energy to ions in a mass spectrometer. MS MS:1000304 accelerating voltage The electrical potential used to impart kinetic energy to ions in a mass spectrometer. PSI:MS OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB. MS MS:1000305 This child of the former purgatory term m/z Separation Method was made obsolete. cyclotron motion true OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB. PSI:MS OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time. MS MS:1000306 This child of the former purgatory term mass spectrometer was made obsolete. dynamic mass spectrometry true OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time. PSI:MS Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle. MS MS:1000307 einzel lens Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle. PSI:MS The magnitude of the force per unit charge at a given point in space. MS MS:1000308 electric field strength The magnitude of the force per unit charge at a given point in space. PSI:MS The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole. MS MS:1000309 first stability region The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole. PSI:MS The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element. MS MS:1000310 fringing field The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element. PSI:MS A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field. MS MS:1000311 kinetic energy analyzer A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field. PSI:MS OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer. MS MS:1000312 This former purgatory term was made obsolete. mass limit true OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer. PSI:MS OBSOLETE The limit of m/z over which a mass spectrometer can detect ions. MS MS:1000313 This former purgatory term was made obsolete. scan m/z range? true OBSOLETE The limit of m/z over which a mass spectrometer can detect ions. PSI:MS OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap. MS MS:1000314 This child of the former purgatory term m/z Separation Method was made obsolete. mass selective axial ejection true OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap. PSI:MS OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap. MS MS:1000315 This child of the former purgatory term m/z Separation Method was made obsolete. mass selective instability true OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap. PSI:MS OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer. MS MS:1000316 This child of the former purgatory term m/z Separation Method was made obsolete. mathieu stability diagram true OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer. PSI:MS OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage. MS MS:1000317 This child of the former purgatory term m/z Separation Method was made obsolete. orthogonal extraction true OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage. PSI:MS OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it. MS MS:1000318 This child of the former purgatory term m/z Separation Method was made obsolete. resonance ion ejection true OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it. PSI:MS The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time. MS MS:1000319 space charge effect The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time. PSI:MS An electric or magnetic field that does not change in time. MS MS:1000320 static field An electric or magnetic field that does not change in time. PSI:MS OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained. MS MS:1000321 This child of the former purgatory term m/z Separation Method was made obsolete. 2E Mass Spectrum true OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained. PSI:MS The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z. MS MS:1000322 charge inversion mass spectrum The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z. PSI:MS OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement. MS constant neutral mass loss scan fixed neutral fragment scan MS:1000323 This former purgatory term was made obsolete. constant neutral loss scan true OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement. PSI:MS OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment. Constant Neutral Mass Gain Scan MS MS:1000324 This former purgatory term was made obsolete. constant neutral gain scan true OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment. PSI:MS A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell. constant neutral mass gain spectrum MS MS:1000325 constant neutral gain spectrum A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell. PSI:MS A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. constant neutral mass loss spectrum MS MS:1000326 constant neutral loss spectrum A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. PSI:MS OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. MS MS:1000327 This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244). consecutive reaction monitoring true OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. PSI:MS A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions. MS MS:1000328 e/2 mass spectrum A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions. PSI:MS OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum. MS MS:1000329 This former purgatory term was made obsolete. linked scan true OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum. PSI:MS OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. MS MS:1000330 This child of the former purgatory term linked scan was made obsolete. linked scan at constant b/e true OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. PSI:MS OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors. MS MS:1000331 This child of the former purgatory term linked scan was made obsolete. Linked Scan at Constant E2/V true OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors. PSI:MS OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended. MS MS:1000332 This child of the former purgatory term linked scan was made obsolete. Linked Scan at Constant B2/E true OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended. PSI:MS OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan. MS MS:1000333 This child of the former purgatory term linked scan was made obsolete. Linked Scan at Constant B[1-(E/E0)]^1/2 / E true OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan. PSI:MS OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time. MS MS:1000334 This child of the former purgatory term m/z Separation Method was made obsolete. MS/MS in Time true OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time. PSI:MS OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition. MS MS:1000335 This child of the former purgatory term m/z Separation Method was made obsolete. MS/MS in Space true OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition. PSI:MS The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type). MS MS:1000336 neutral loss The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type). PSI:MS OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated. MS granddaughter ion MS:1000337 This child of the former purgatory term product ion was made obsolete. nth generation product ion true OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated. PSI:MS OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions. MS MS:1000338 This former purgatory term was made obsolete. nth generation product ion scan true OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions. PSI:MS OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions. MS MS:1000339 This term was made obsolete because it was merged with MSn spectrum (MS:1000580). nth generation product ion spectrum true OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions. PSI:MS OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated. MS parent ion MS:1000340 This child of the former purgatory term ion role was made obsolete. precursor ion true OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated. PSI:MS Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z. MS MS:1000341 precursor ion spectrum Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z. PSI:MS OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated. MS daughter ion MS:1000342 This child of the former purgatory term ion role was made obsolete. product ion true OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated. PSI:MS OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions. MS MS:1000343 This term was made obsolete because it was merged with MSn spectrum (MS:1000580). product ion spectrum true OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions. PSI:MS OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+. Progeny Fragment Ion MS MS:1000344 This child of the former purgatory term ion chemical type was made obsolete. progeny ion true OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+. PSI:MS Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector. MS MS:1000345 array detector Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector. PSI:MS A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected. MS MS:1000346 conversion dynode A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected. PSI:MS One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode. MS MS:1000347 dynode One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode. PSI:MS A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. MS MS:1000348 focal plane collector A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. PSI:MS A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier. MS MS:1000349 ion-to-photon detector A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier. PSI:MS A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially. MS MS:1000350 point collector A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially. PSI:MS A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector. MS MS:1000351 postacceleration detector A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector. PSI:MS OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go. MS MS:1000352 This former purgatory term was made obsolete. secondary electron true OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go. PSI:MS Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules. MS MS:1000353 adduct ion Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules. PSI:MS OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure. MS MS:1000354 This child of the former purgatory term ion chemical type was made obsolete. aromatic ion true OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure. PSI:MS OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+. MS MS:1000355 This child of the former purgatory term ion chemical type was made obsolete. analog ion true OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+. PSI:MS OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic. MS MS:1000356 This child of the former purgatory term ion chemical type was made obsolete. anti-aromatic ion true OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic. PSI:MS OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used. MS MS:1000357 This child of the former purgatory term ion chemical type was made obsolete. cationized molecule true OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used. PSI:MS OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-. MS MS:1000358 This child of the former purgatory term ion chemical type was made obsolete. cluster ion true OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-. PSI:MS OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion. MS MS:1000359 This child of the former purgatory term ion chemical type was made obsolete. Conventional ion true OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion. PSI:MS OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives. MS MS:1000360 This child of the former purgatory term ion chemical type was made obsolete. diagnostic ion true OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives. PSI:MS OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+. MS MS:1000361 This child of the former purgatory term ion chemical type was made obsolete. dimeric ion true OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+. PSI:MS OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion. MS MS:1000362 This child of the former purgatory term ion chemical type was made obsolete. distonic ion true OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion. PSI:MS OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions. MS MS:1000363 This child of the former purgatory term ion chemical type was made obsolete. enium ion true OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions. PSI:MS OBSOLETE A product ion that results from the dissociation of a precursor ion. MS MS:1000364 This term was made obsolete because it was replaced by product ion (MS:1000342). fragment ion true OBSOLETE A product ion that results from the dissociation of a precursor ion. PSI:MS OBSOLETE An atomic or molecular species having a net positive or negative electric charge. MS MS:1000365 This former purgatory term was made obsolete. ion? true OBSOLETE An atomic or molecular species having a net positive or negative electric charge. PSI:MS OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue. MS MS:1000366 This child of the former purgatory term ion chemical type was made obsolete. Isotopologue ion true OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue. PSI:MS OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer. MS MS:1000367 This child of the former purgatory term ion chemical type was made obsolete. Isotopomeric ion true OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer. PSI:MS OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection. MS MS:1000368 This child of the former purgatory term ion stability type was made obsolete. metastable ion true OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection. PSI:MS OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion. MS MS:1000369 This child of the former purgatory term ion chemical type was made obsolete. molecular ion true OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion. PSI:MS OBSOLETE An atomic or molecular species having a net negative electric charge. MS MS:1000370 This child of the former purgatory term ion chemical type was made obsolete. negative ion true OBSOLETE An atomic or molecular species having a net negative electric charge. PSI:MS OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions. MS MS:1000371 This child of the former purgatory term ion chemical type was made obsolete. non-classical ion true OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions. PSI:MS OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+. MS MS:1000372 This child of the former purgatory term ion chemical type was made obsolete. onium ion true OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+. PSI:MS OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions. MS MS:1000373 This child of the former purgatory term ion chemical type was made obsolete. principal ion true OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions. PSI:MS OBSOLETE An atomic or molecular species having a net positive electric charge. MS MS:1000374 This child of the former purgatory term ion chemical type was made obsolete. positive ion true OBSOLETE An atomic or molecular species having a net positive electric charge. PSI:MS OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended. MS MS:1000375 This child of the former purgatory term ion chemical type was made obsolete. protonated molecule true OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended. PSI:MS OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation. MS MS:1000376 This child of the former purgatory term ion chemical type was made obsolete. radical ion true OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation. PSI:MS OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion. MS MS:1000377 This child of the former purgatory term ion chemical type was made obsolete. reference ion true OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion. PSI:MS OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer. MS MS:1000378 This child of the former purgatory term ion stability type was made obsolete. stable ion true OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer. PSI:MS OBSOLETE An ion with sufficient energy to dissociate within the ion source. MS MS:1000379 This child of the former purgatory term ion stability type was made obsolete. unstable ion true OBSOLETE An ion with sufficient energy to dissociate within the ion source. PSI:MS A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state. MS MS:1000380 adiabatic ionization A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state. PSI:MS An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron. MS MS:1000381 associative ionization An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron. PSI:MS Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. MS MS:1000382 atmospheric pressure photoionization Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. PSI:MS The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source. MS MS:1000383 autodetachment The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source. PSI:MS The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source. MS MS:1000384 autoionization The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source. PSI:MS The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization. MS MS:1000385 charge exchange ionization The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization. PSI:MS The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization. MS MS:1000386 chemi-ionization The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization. PSI:MS The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface. MS MS:1000387 desorption/ionization on silicon The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface. PSI:MS The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion. MS MS:1000388 dissociative ionization The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion. PSI:MS The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. MS MS:1000389 electron ionization The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. PSI:MS OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules. MS MS:1000390 This child of the former purgatory term ion reaction was made obsolete. ion desolvation true OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules. PSI:MS OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products. MS MS:1000391 This child of the former purgatory term ion reaction was made obsolete. ion-pair formation true OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products. PSI:MS The ratio of the number of ions formed to the number of electrons, molecules or photons used. MS MS:1000392 ionization efficiency The ratio of the number of ions formed to the number of electrons, molecules or photons used. PSI:MS The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material. MS MS:1000393 laser desorption ionization The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material. PSI:MS No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing. MS MS:1000394 no sequence database No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing. PSI:PI The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization. MS MS:1000395 liquid secondary ionization The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization. PSI:MS A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source. MS MS:1000396 membrane inlet A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source. PSI:MS Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray. MS MS:1000397 microelectrospray Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray. PSI:MS Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray. nanospray MS MS:1000398 nanoelectrospray Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray. PSI:MS Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited. MS MS:1000399 penning ionization Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited. PSI:MS The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. MS MS:1000400 plasma desorption ionization The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. PSI:MS OBSOLETE An electronic state capable of undergoing auto-Ionization. MS MS:1000401 This child of the former purgatory term ion reaction was made obsolete. pre-ionization state true OBSOLETE An electronic state capable of undergoing auto-Ionization. PSI:MS The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions. MS MS:1000402 secondary ionization The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions. PSI:MS The formation of gas-phase ions without extensive fragmentation. MS MS:1000403 soft ionization The formation of gas-phase ions without extensive fragmentation. PSI:MS The formation of ions from a solid material by an intermittent electrical discharge. MS MS:1000404 spark ionization The formation of ions from a solid material by an intermittent electrical discharge. PSI:MS The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization. MS MS:1000405 surface-assisted laser desorption ionization The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization. PSI:MS The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. MS MS:1000406 surface ionization The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. PSI:MS The ionization of a neutral species through contact with a high temperature surface. MS MS:1000407 thermal ionization The ionization of a neutral species through contact with a high temperature surface. PSI:MS A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state. MS MS:1000408 vertical ionization A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state. PSI:MS OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion. MS MS:1000409 This child of the former purgatory term ion reaction was made obsolete. association reaction true OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion. PSI:MS OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds. MS MS:1000410 This child of the former purgatory term ion reaction was made obsolete. alpha-cleavage true OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds. PSI:MS OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds. MS MS:1000411 This child of the former purgatory term ion reaction was made obsolete. beta-cleavage true OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds. PSI:MS An inert gas used for collisional deactivation of internally excited ions. MS MS:1000412 buffer gas An inert gas used for collisional deactivation of internally excited ions. PSI:MS OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation. MS MS:1000413 This child of the former purgatory term ion reaction was made obsolete. charge-induced fragmentation true OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation. PSI:MS OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion. MS MS:1000414 This child of the former purgatory term ion reaction was made obsolete. charge inversion reaction true OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion. PSI:MS OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion. MS MS:1000415 This child of the former purgatory term ion reaction was made obsolete. charge permutation reaction true OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion. PSI:MS OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion. MS MS:1000416 This child of the former purgatory term ion reaction was made obsolete. charge stripping reaction true OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion. PSI:MS OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species. MS MS:1000417 This child of the former purgatory term ion reaction was made obsolete. charge transfer reaction true OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species. PSI:MS OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion. MS MS:1000418 This child of the former purgatory term ion reaction was made obsolete. collisional excitation true OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion. PSI:MS An inert gas used for collisional excitation. The term target gas is not recommended. MS MS:1000419 collision gas An inert gas used for collisional excitation. The term target gas is not recommended. PSI:MS OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis. MS heterolysis MS:1000420 This child of the former purgatory term ion reaction was made obsolete. heterolytic cleavage true OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis. PSI:MS OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV. MS MS:1000421 This child of the former purgatory term ion reaction was made obsolete. high energy collision true OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV. PSI:MS A collision-induced dissociation process that occurs in a beam-type collision cell. HCD MS MS:1000422 beam-type collision-induced dissociation A collision-induced dissociation process that occurs in a beam-type collision cell. PSI:MS OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis. MS homolysis MS:1000423 This child of the former purgatory term ion reaction was made obsolete. homolytic cleavage true OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis. PSI:MS OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer. MS MS:1000424 This child of the former purgatory term ion reaction was made obsolete. hydrogen/deuterium exchange true OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer. PSI:MS OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species. MS MS:1000425 This former purgatory term was made obsolete. ion energy loss spectrum true OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species. PSI:MS OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral. MS MS:1000426 This child of the former purgatory term ion reaction was made obsolete. ionizing collision true OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral. PSI:MS OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule. MS MS:1000427 This child of the former purgatory term ion reaction was made obsolete. ion/molecule reaction true OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule. PSI:MS OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions. MS MS:1000428 This child of the former purgatory term ion reaction was made obsolete. ion/neutral complex true OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions. PSI:MS OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants. MS MS:1000429 This child of the former purgatory term ion reaction was made obsolete. ion/neutral species reaction true OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants. PSI:MS OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product. MS MS:1000430 This child of the former purgatory term ion reaction was made obsolete. ion/neutral species exchange reaction true OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product. PSI:MS OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account. MS MS:1000431 This child of the former purgatory term ion reaction was made obsolete. kinetic method true OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account. PSI:MS OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower. MS MS:1000432 This child of the former purgatory term ion reaction was made obsolete. low energy collisions true OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower. PSI:MS A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative. MS MS:1000433 low-energy collision-induced dissociation A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative. PSI:MS OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied. MS MS:1000434 This child of the former purgatory term ion reaction was made obsolete. McLafferty Rearrangement true OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied. PSI:MS A process wherein the reactant ion is dissociated as a result of absorption of one or more photons. MPD multiphoton dissociation MS MS:1000435 photodissociation A process wherein the reactant ion is dissociated as a result of absorption of one or more photons. PSI:MS OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral. MS MS:1000436 This child of the former purgatory term ion reaction was made obsolete. partial charge transfer reaction true OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral. PSI:MS OBSOLETE Chemical transformation involving an ion. MS MS:1000437 This child of the former purgatory term ion was made obsolete. ion reaction true OBSOLETE Chemical transformation involving an ion. PSI:MS OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners. MS MS:1000438 This child of the former purgatory term ion reaction was made obsolete. superelastic collision true OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners. PSI:MS OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion. MS MS:1000439 This child of the former purgatory term ion reaction was made obsolete. surface-induced reaction true OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion. PSI:MS OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion. MS MS:1000440 This child of the former purgatory term ion reaction was made obsolete. unimolecular dissociation true OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion. PSI:MS Function or process of the mass spectrometer where it records a spectrum. MS MS:1000441 scan Function or process of the mass spectrometer where it records a spectrum. PSI:MS Representation of intensity values corresponding to a range of measurement space. MS MS:1000442 spectrum Representation of intensity values corresponding to a range of measurement space. PSI:MS Mass analyzer separates the ions according to their mass-to-charge ratio. MS MS:1000443 mass analyzer type Mass analyzer separates the ions according to their mass-to-charge ratio. PSI:MS OBSOLETE Mass/charge separation Method. MS MS:1000444 This former purgatory term was made obsolete. m/z Separation Method true OBSOLETE Mass/charge separation Method. PSI:MS OBSOLETE Sequential m/z separation method. MS MS:1000445 This former purgatory term was made obsolete. sequential m/z separation method true OBSOLETE Sequential m/z separation method. PSI:MS The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample. FIB MS MS:1000446 fast ion bombardment The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample. PSI:MS Finnigan LTQ MS. MS MS:1000447 LTQ Finnigan LTQ MS. PSI:MS Finnigan LTQ FT MS. MS MS:1000448 LTQ FT Finnigan LTQ FT MS. PSI:MS Finnigan LTQ Orbitrap MS. MS MS:1000449 LTQ Orbitrap Finnigan LTQ Orbitrap MS. PSI:MS Finnigan LXQ MS. MS MS:1000450 LXQ Finnigan LXQ MS. PSI:MS Terms used to describe the Analyzer. analyzer MS MS:1000451 mass analyzer Terms used to describe the Analyzer. PSI:MS Terms used to describe types of data processing. data processing MS MS:1000452 data transformation Terms used to describe types of data processing. PSI:MS The device that detects ions. MS MS:1000453 detector The device that detects ions. PSI:MS OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5. MS MS:1000454 This former purgatory term was made obsolete. instrument additional description true OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5. PSI:MS Ion selection properties that are associated with a value. MS MS:1000455 ion selection attribute Ion selection properties that are associated with a value. PSI:MS Terms to describe the precursor activation. activation MS MS:1000456 precursor activation Terms to describe the precursor activation. PSI:MS Terms to describe the sample. MS MS:1000457 sample Terms to describe the sample. PSI:MS Terms to describe the source. MS MS:1000458 source Terms to describe the source. PSI:MS OBSOLETE Terms used to describe the spectrum. MS MS:1000459 This former purgatory term was made obsolete. spectrum instrument description true OBSOLETE Terms used to describe the spectrum. PSI:MS OBSOLETE Terms to describe units. MS MS:1000460 This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000). unit true OBSOLETE Terms to describe units. PSI:MS OBSOLETE Terms to describe Additional. MS MS:1000461 This former purgatory term was made obsolete. additional description true OBSOLETE Terms to describe Additional. PSI:MS Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions. MS MS:1000462 ion optics Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions. PSI:MS Description of the instrument or the mass spectrometer. instrument configuration MS MS:1000463 instrument Description of the instrument or the mass spectrometer. PSI:MS OBSOLETE A unit of measurement for mass. MS MS:1000464 This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002). mass unit true OBSOLETE A unit of measurement for mass. PSI:MS Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer. MS MS:1000465 scan polarity Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer. PSI:MS OBSOLETE Alternating. MS MS:1000466 This term was made obsolete because . alternating true OBSOLETE Alternating. PSI:MS The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2. MS MS:1000467 1200 series LC/MSD SL The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2. PSI:MS The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications. MS MS:1000468 6110 Quadrupole LC/MS The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications. PSI:MS The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition. MS MS:1000469 6120A Quadrupole LC/MS The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition. PSI:MS The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition. MS MS:1000470 6130 Quadrupole LC/MS The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition. PSI:MS The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition. MS MS:1000471 6140 Quadrupole LC/MS The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition. PSI:MS The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. MS MS:1000472 6210 Time-of-Flight LC/MS The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. PSI:MS The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges. MS MS:1000473 6310 Ion Trap LC/MS The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges. PSI:MS The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. MS MS:1000474 6320 Ion Trap LC/MS The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. PSI:MS The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. MS MS:1000475 6330 Ion Trap LC/MS The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. PSI:MS The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. MS MS:1000476 6340 Ion Trap LC/MS The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. PSI:MS The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration. 6410 Triple Quad LC/MS MS MS:1000477 6410 Triple Quadrupole LC/MS The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration. PSI:MS The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor. MS MS:1000478 1200 series LC/MSD VL The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor. PSI:MS OBSOLETE Terms that will likely become obsolete unless there are wails of dissent. MS MS:1000479 The whole branch purgatory term was made obsolete. purgatory true OBSOLETE Terms that will likely become obsolete unless there are wails of dissent. PSI:MS Analyzer properties that are associated with a value. MS MS:1000480 mass analyzer attribute Analyzer properties that are associated with a value. PSI:MS Detector attribute recognized as a value. MS MS:1000481 detector attribute Detector attribute recognized as a value. PSI:MS Property of a source device that need a value. MS MS:1000482 source attribute Property of a source device that need a value. PSI:MS Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific. MS Thermo Scientific MS:1000483 Thermo Fisher Scientific instrument model Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific. PSI:MS An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer. MS MS:1000484 orbitrap An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer. PSI:MS Nanospray Inlet. MS MS:1000485 nanospray inlet Nanospray Inlet. PSI:MS Potential difference at the MS source in volts. MS MS:1000486 source potential Potential difference at the MS source in volts. PSI:MS Ion optics involves components that help focus ion streams in mass spectrometry. MS MS:1000487 ion optics attribute Ion optics involves components that help focus ion streams in mass spectrometry. PSI:MS Hitachi instrument model. MS MS:1000488 Hitachi instrument model Hitachi instrument model. PSI:MS Varian instrument model. MS MS:1000489 Varian instrument model Varian instrument model. PSI:MS Agilent instrument model. MS MS:1000490 Agilent instrument model Agilent instrument model. PSI:MS Dionex instrument model. MS MS:1000491 Dionex instrument model Dionex instrument model. PSI:MS Thermo Electron Corporation instrument model. MS MS:1000492 Thermo Electron instrument model Thermo Electron Corporation instrument model. PSI:MS Finnigan MAT instrument model. MS MS:1000493 Finnigan MAT instrument model Finnigan MAT instrument model. PSI:MS Thermo Scientific instrument model. MS MS:1000494 Thermo Scientific instrument model Thermo Scientific instrument model. PSI:MS Applied Biosystems instrument model. ABI MS MS:1000495 Applied Biosystems instrument model Applied Biosystems instrument model. PSI:MS Instrument properties that are associated with a value. MS MS:1000496 instrument attribute Instrument properties that are associated with a value. PSI:MS Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate. enhanced resolution scan MS MS:1000497 zoom scan Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate. PSI:MS OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range. MS MS:1000498 This former purgatory term was made obsolete. full scan true OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range. PSI:MS Nonphysical characteristic attributed to a spectrum. MS MS:1000499 spectrum attribute Nonphysical characteristic attributed to a spectrum. PSI:MS The upper m/z bound of a mass spectrometer scan window. MS mzRangeStop MS:1000500 scan window upper limit The upper m/z bound of a mass spectrometer scan window. PSI:MS The lower m/z bound of a mass spectrometer scan window. MS mzRangeStart MS:1000501 scan window lower limit The lower m/z bound of a mass spectrometer scan window. PSI:MS The time spent gathering data across a peak. MS Scan Duration MS:1000502 dwell time The time spent gathering data across a peak. PSI:MS Nonphysical characteristic attributed to a spectrum acquisition scan. MS MS:1000503 scan attribute Nonphysical characteristic attributed to a spectrum acquisition scan. PSI:MS M/z value of the signal of highest intensity in the mass spectrum. MS MS:1000504 base peak m/z M/z value of the signal of highest intensity in the mass spectrum. PSI:MS The intensity of the greatest peak in the mass spectrum. MS MS:1000505 base peak intensity The intensity of the greatest peak in the mass spectrum. PSI:MS OBSOLETE Ion Role. MS MS:1000506 This child of the former purgatory term ion was made obsolete. ion role true OBSOLETE Ion Role. PSI:MS Nonphysical characteristic attributed to an ion. MS MS:1000507 ion property Nonphysical characteristic attributed to an ion. PSI:MS OBSOLETE Ion Type. MS MS:1000508 This child of the former purgatory term ion was made obsolete. ion chemical type true OBSOLETE Ion Type. PSI:MS Activation Energy. MS MS:1000509 activation energy Activation Energy. PSI:MS Precursor Activation Attribute. MS MS:1000510 precursor activation attribute Precursor Activation Attribute. PSI:MS Stage number achieved in a multi stage mass spectrometry acquisition. MS MS:1000511 ms level Stage number achieved in a multi stage mass spectrometry acquisition. PSI:MS A string unique to Thermo instrument describing instrument settings for the scan. MS MS:1000512 filter string A string unique to Thermo instrument describing instrument settings for the scan. PSI:MS A data array of values. MS MS:1000513 binary data array A data array of values. PSI:MS A data array of m/z values. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000514 m/z array A data array of m/z values. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of intensity values. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000515 intensity array A data array of intensity values. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of charge values. binary-data-type:MS:1000519 MS MS:1000516 charge array A data array of charge values. PSI:MS binary-data-type:MS:1000519 32-bit integer A data array of signal-to-noise values. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000517 signal to noise array A data array of signal-to-noise values. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float. MS MS:1000518 binary data type Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float. PSI:MS Signed 32-bit little-endian integer. MS MS:1000519 32-bit integer Signed 32-bit little-endian integer. PSI:MS OBSOLETE Signed 16-bit float. MS MS:1000520 16-bit float true OBSOLETE Signed 16-bit float. PSI:MS 32-bit precision little-endian floating point conforming to IEEE-754. MS MS:1000521 32-bit float 32-bit precision little-endian floating point conforming to IEEE-754. PSI:MS Signed 64-bit little-endian integer. MS MS:1000522 64-bit integer Signed 64-bit little-endian integer. PSI:MS 64-bit precision little-endian floating point conforming to IEEE-754. MS MS:1000523 64-bit float 64-bit precision little-endian floating point conforming to IEEE-754. PSI:MS Describes the data content on the file. MS MS:1000524 data file content Describes the data content on the file. PSI:MS Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks. MS MS:1000525 spectrum representation Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks. PSI:MS Waters data file format found in a Waters RAW directory, generated from an MS acquisition. MS MS:1000526 Waters raw format Waters data file format found in a Waters RAW directory, generated from an MS acquisition. PSI:MS Highest m/z value observed in the m/z array. MS MS:1000527 highest observed m/z Highest m/z value observed in the m/z array. PSI:MS Lowest m/z value observed in the m/z array. MS MS:1000528 lowest observed m/z Lowest m/z value observed in the m/z array. PSI:MS Serial Number of the instrument. MS MS:1000529 instrument serial number Serial Number of the instrument. PSI:MS Conversion of one file format to another. MS MS:1000530 file format conversion Conversion of one file format to another. PSI:MS Software related to the recording or transformation of spectra. MS MS:1000531 software Software related to the recording or transformation of spectra. PSI:MS Thermo Finnigan software for data acquisition and analysis. MS MS:1000532 Xcalibur Thermo Finnigan software for data acquisition and analysis. PSI:MS Thermo Finnigan software for data analysis of peptides and proteins. MS Bioworks Browser MS:1000533 Bioworks Thermo Finnigan software for data analysis of peptides and proteins. PSI:MS Micromass software for data acquisition and analysis. MS MS:1000534 MassLynx Micromass software for data acquisition and analysis. PSI:MS Bruker software for data analysis. MS MS:1000535 FlexAnalysis Bruker software for data analysis. PSI:MS Applied Biosystems software for data acquisition and analysis. MS MS:1000536 Data Explorer Applied Biosystems software for data acquisition and analysis. PSI:MS Applied Biosystems software for data acquisition and analysis. MS MS:1000537 4700 Explorer Applied Biosystems software for data acquisition and analysis. PSI:MS A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology. wolf MS MS:1000538 massWolf A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology. PSI:MS Applied Biosystems MALDI-TOF data acquisition and analysis system. MS MS:1000539 Voyager Biospectrometry Workstation System Applied Biosystems MALDI-TOF data acquisition and analysis system. PSI:MS Bruker software for data acquisition. MS MS:1000540 FlexControl Bruker software for data acquisition. PSI:MS A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced "readraw". MS MS:1000541 ReAdW A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced "readraw". PSI:MS A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program. MS MS:1000542 MzStar A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program. PSI:MS Data processing attribute used to describe the type of data processing performed on the data file. MS MS:1000543 data processing action Data processing attribute used to describe the type of data processing performed on the data file. PSI:MS Conversion of a file format to Proteomics Standards Initiative mzML file format. MS MS:1000544 Conversion to mzML Conversion of a file format to Proteomics Standards Initiative mzML file format. PSI:MS Conversion of a file format to Institute of Systems Biology mzXML file format. MS MS:1000545 Conversion to mzXML Conversion of a file format to Institute of Systems Biology mzXML file format. PSI:MS Conversion of a file format to Proteomics Standards Initiative mzData file format. MS MS:1000546 Conversion to mzData Conversion of a file format to Proteomics Standards Initiative mzData file format. PSI:MS Object Attribute. MS MS:1000547 object attribute Object Attribute. PSI:MS Sample properties that are associated with a value. MS MS:1000548 sample attribute Sample properties that are associated with a value. PSI:MS Selection window properties that are associated with a value. MS MS:1000549 selection window attribute Selection window properties that are associated with a value. PSI:MS OBSOLETE Time Unit. MS MS:1000550 This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003). time unit true OBSOLETE Time Unit. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition. MS MS:1000551 Analyst SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition. PSI:MS OBSOLETE Maldi Spot Identifier. MS MS:1000552 This former purgatory term was made obsolete. maldi spot identifier true OBSOLETE Maldi Spot Identifier. PSI:MS A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology. MS MS:1000553 Trapper A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology. PSI:MS ThermoFinnigan LCQ Deca. MS MS:1000554 LCQ Deca ThermoFinnigan LCQ Deca. PSI:MS LTQ Orbitrap Discovery. MS MS:1000555 LTQ Orbitrap Discovery LTQ Orbitrap Discovery. PSI:MS LTQ Orbitrap XL. MS MS:1000556 LTQ Orbitrap XL LTQ Orbitrap XL. PSI:MS LTQ FT Ultra. MS MS:1000557 LTQ FT Ultra LTQ FT Ultra. PSI:MS GC Quantum. MS MS:1000558 GC Quantum GC Quantum. PSI:MS Spectrum type. MS MS:1000559 spectrum type Spectrum type. PSI:MS The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. MS MS:1000560 mass spectrometer file format The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. PSI:MS Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data. MS MS:1000561 data file checksum type Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data. PSI:MS Applied Biosystems WIFF file format. MS MS:1000562 ABI WIFF format Applied Biosystems WIFF file format. PSI:MS Thermo Scientific RAW file format. MS MS:1000563 Thermo RAW format Thermo Scientific RAW file format. PSI:MS Proteomics Standards Inititative mzData file format. MS MS:1000564 PSI mzData format Proteomics Standards Inititative mzData file format. PSI:MS Micromass PKL file format. MS MS:1000565 Micromass PKL format Micromass PKL file format. PSI:MS Institute of Systems Biology mzXML file format. MS MS:1000566 ISB mzXML format Institute of Systems Biology mzXML file format. PSI:MS Bruker/Agilent YEP file format. MS MS:1000567 Bruker/Agilent YEP format Bruker/Agilent YEP file format. PSI:MS MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files. MS MS:1000568 MD5 MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files. PSI:MS SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard. MS MS:1000569 SHA-1 SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard. PSI:MS Method used to combine the mass spectra. MS MS:1000570 spectra combination Method used to combine the mass spectra. PSI:MS Spectra Sum. MS MS:1000571 sum of spectra Spectra Sum. PSI:MS Compression Type. MS MS:1000572 binary data compression type Compression Type. PSI:MS Spectra is combined by calculating the median of the spectra. MS MS:1000573 median of spectra Spectra is combined by calculating the median of the spectra. PSI:MS Zlib. MS MS:1000574 zlib compression Zlib. PSI:MS Spectra is combined by calculating the mean of the spectra. MS MS:1000575 mean of spectra Spectra is combined by calculating the mean of the spectra. PSI:MS No Compression. MS MS:1000576 no compression No Compression. PSI:MS Data file from which an entity is sourced. source file MS MS:1000577 source data file Data file from which an entity is sourced. PSI:MS LCQ Fleet. MS MS:1000578 LCQ Fleet LCQ Fleet. PSI:MS Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment. Q1 spectrum Q3 spectrum Single-Stage Mass Spectrometry full spectrum MS MS:1000579 MS1 spectrum Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment. PSI:MS MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n. multiple-stage mass spectrometry spectrum nth generation product ion spectrum product ion spectrum MS MS:1000580 MSn spectrum MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n. PSI:MS Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. MS MS:1000581 CRM spectrum Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. PSI:MS Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring). MIM spectrum multiple ion monitoring spectrum selected ion monitoring spectrum MS MS:1000582 SIM spectrum Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring). PSI:MS Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space. MRM spectrum multiple reaction monitoring spectrum selected reaction monitoring spectrum MS MS:1000583 SRM spectrum Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space. PSI:MS Proteomics Standards Inititative mzML file format. MS MS:1000584 mzML format Proteomics Standards Inititative mzML file format. PSI:MS Details about a person or organization to contact in case of concern or discussion about the file. MS MS:1000585 contact attribute Details about a person or organization to contact in case of concern or discussion about the file. PSI:MS Name of the contact person or organization. MS MS:1000586 contact name Name of the contact person or organization. PSI:MS Postal address of the contact person or organization. MS MS:1000587 contact address Postal address of the contact person or organization. PSI:MS Uniform Resource Locator related to the contact person or organization. MS MS:1000588 contact URL Uniform Resource Locator related to the contact person or organization. PSI:MS Email address of the contact person or organization. MS MS:1000589 contact email Email address of the contact person or organization. PSI:MS Home institution of the contact person. MS MS:1000590 contact affiliation Home institution of the contact person. PSI:MS A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program. MS MS:1000591 MzWiff A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program. PSI:MS A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process. MS MS:1000592 smoothing A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process. PSI:MS A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values. MS MS:1000593 baseline reduction A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values. PSI:MS The removal of very low intensity data points that are likely to be spurious noise rather than real signal. thresholding MS MS:1000594 low intensity data point removal The removal of very low intensity data points that are likely to be spurious noise rather than real signal. PSI:MS A data array of relative time offset values from a reference time. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000595 time array A data array of relative time offset values from a reference time. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float An attribute of resolution when recording the detector response in absence of the analyte. MS MS:1000596 measurement method An attribute of resolution when recording the detector response in absence of the analyte. PSI:MS The electrical potential used to impart kinetic energy to ions in a mass spectrometer. MS MS:1000597 ion optics type The electrical potential used to impart kinetic energy to ions in a mass spectrometer. PSI:MS A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions. ETD MS MS:1000598 electron transfer dissociation A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions. DOI:10.1073/pnas.0402700101 PMID:15210983 PSI:MS A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected. PQD MS MS:1000599 pulsed q dissociation A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected. PSI:MS Database application and analysis platform for proteomics. MS MS:1000600 Proteios Database application and analysis platform for proteomics. PSI:MS source:http://www.proteios.org Waters software for data analysis. MS MS:1000601 ProteinLynx Global Server Waters software for data analysis. PSI:MS Shimadzu MALDI-TOF instrument model. MS MS:1000602 Shimadzu MALDI-TOF instrument model Shimadzu MALDI-TOF instrument model. PSI:MS Shimadzu Scientific Instruments instrument model. MS MS:1000603 Shimadzu Scientific Instruments instrument model Shimadzu Scientific Instruments instrument model. PSI:MS Shimadzu Scientific Instruments LCMS-IT-TOF MS. MS MS:1000604 LCMS-IT-TOF Shimadzu Scientific Instruments LCMS-IT-TOF MS. PSI:MS Shimadzu Scientific Instruments LCMS-2010EV MS. MS MS:1000605 LCMS-2010EV Shimadzu Scientific Instruments LCMS-2010EV MS. PSI:MS Shimadzu Scientific Instruments LCMS-2010A MS. MS MS:1000606 LCMS-2010A Shimadzu Scientific Instruments LCMS-2010A MS. PSI:MS Shimadzu Biotech AXIMA CFR MALDI-TOF MS. MS MS:1000607 AXIMA CFR MALDI-TOF Shimadzu Biotech AXIMA CFR MALDI-TOF MS. PSI:MS Shimadzu Biotech AXIMA-QIT MS. MS MS:1000608 AXIMA-QIT Shimadzu Biotech AXIMA-QIT MS. PSI:MS Shimadzu Biotech AXIMA-CFR plus MS. MS MS:1000609 AXIMA-CFR plus Shimadzu Biotech AXIMA-CFR plus MS. PSI:MS Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS. MS MS:1000610 AXIMA Performance MALDI-TOF/TOF Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS. PSI:MS Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS. MS MS:1000611 AXIMA Confidence MALDI-TOF Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS. PSI:MS Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS. MS MS:1000612 AXIMA Assurance Linear MALDI-TOF Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS. PSI:MS SEQUEST DTA file format. MS MS:1000613 DTA format SEQUEST DTA file format. PSI:MS Peak list file format used by ProteinLynx Global Server. MS MS:1000614 ProteinLynx Global Server mass spectrum XML format Peak list file format used by ProteinLynx Global Server. PSI:MS ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb. pwiz MS MS:1000615 ProteoWizard software ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb. PSI:MS A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo "scan event", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time. MS MS:1000616 preset scan configuration A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo "scan event", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time. PSI:MS A data array of electromagnetic radiation wavelength values. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000617 wavelength array A data array of electromagnetic radiation wavelength values. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float Highest wavelength observed in an EMR spectrum. MS MS:1000618 highest observed wavelength Highest wavelength observed in an EMR spectrum. PSI:MS Lowest wavelength observed in an EMR spectrum. MS MS:1000619 lowest observed wavelength Lowest wavelength observed in an EMR spectrum. PSI:MS OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum). MS MS:1000620 This term was made obsolete because it was replaced by absorption spectrum (MS:1000806). PDA spectrum true OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum). PSI:MS An array detector used to record spectra in the ultraviolet and visible region of light. PDA MS MS:1000621 photodiode array detector An array detector used to record spectra in the ultraviolet and visible region of light. PSI:MS Surveyor PDA. MS MS:1000622 Surveyor PDA Surveyor PDA. PSI:MS Accela PDA. MS MS:1000623 Accela PDA Accela PDA. PSI:MS Inductive detector. image current detector MS MS:1000624 inductive detector Inductive detector. PSI:MS Representation of a chromatographic separation attribute measurement versus time. MS MS:1000625 chromatogram Representation of a chromatographic separation attribute measurement versus time. PSI:MS Type of chromatogram measurement being represented. MS MS:1000626 chromatogram type Type of chromatogram measurement being represented. PSI:MS Representation of an array of the measurements of a specific single ion current versus time. SIC chromatogram MS MS:1000627 selected ion current chromatogram Representation of an array of the measurements of a specific single ion current versus time. PSI:MS Representation of an array of the most intense peaks versus time. MS MS:1000628 basepeak chromatogram Representation of an array of the most intense peaks versus time. PSI:MS Threshold below which some action is taken. MS MS:1000629 low intensity threshold Threshold below which some action is taken. PSI:MS Data processing parameter used in the data processing performed on the data file. MS MS:1000630 data processing parameter Data processing parameter used in the data processing performed on the data file. PSI:MS Threshold above which some action is taken. MS MS:1000631 high intensity threshold Threshold above which some action is taken. PSI:MS Waters oa-ToF based Q-Tof Premier. MS MS:1000632 Q-Tof Premier Waters oa-ToF based Q-Tof Premier. PSI:MS A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty. MS MS:1000633 possible charge state A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty. PSI:MS ThermoFinnigan DSQ GC-MS. MS MS:1000634 DSQ ThermoFinnigan DSQ GC-MS. PSI:MS Thermo Scientific ITQ 700 GC-MS. MS MS:1000635 ITQ 700 Thermo Scientific ITQ 700 GC-MS. PSI:MS Thermo Scientific ITQ 900 GC-MS. MS MS:1000636 ITQ 900 Thermo Scientific ITQ 900 GC-MS. PSI:MS Thermo Scientific ITQ 1100 GC-MS. MS MS:1000637 ITQ 1100 Thermo Scientific ITQ 1100 GC-MS. PSI:MS Thermo Scientific LTQ XL MS with ETD. MS MS:1000638 LTQ XL ETD Thermo Scientific LTQ XL MS with ETD. PSI:MS Thermo Scientific LTQ Orbitrap XL MS with ETD. MS MS:1000639 LTQ Orbitrap XL ETD Thermo Scientific LTQ Orbitrap XL MS with ETD. PSI:MS Thermo Scientific DFS HR GC-MS. MS MS:1000640 DFS Thermo Scientific DFS HR GC-MS. PSI:MS Thermo Scientific DSQ II GC-MS. MS MS:1000641 DSQ II Thermo Scientific DSQ II GC-MS. PSI:MS Thermo Scientific MALDI LTQ XL MS. MS MS:1000642 MALDI LTQ XL Thermo Scientific MALDI LTQ XL MS. PSI:MS Thermo Scientific MALDI LTQ Orbitrap MS. MS MS:1000643 MALDI LTQ Orbitrap Thermo Scientific MALDI LTQ Orbitrap MS. PSI:MS Thermo Scientific TSQ Quantum Access MS. MS MS:1000644 TSQ Quantum Access Thermo Scientific TSQ Quantum Access MS. PSI:MS Thermo Scientific Element XR HR-ICP-MS. MS MS:1000645 Element XR Thermo Scientific Element XR HR-ICP-MS. PSI:MS Thermo Scientific Element 2 HR-ICP-MS. MS MS:1000646 Element 2 Thermo Scientific Element 2 HR-ICP-MS. PSI:MS Thermo Scientific Element GD Glow Discharge MS. MS MS:1000647 Element GD Thermo Scientific Element GD Glow Discharge MS. PSI:MS Thermo Scientific GC IsoLink Isotope Ratio MS. MS MS:1000648 GC IsoLink Thermo Scientific GC IsoLink Isotope Ratio MS. PSI:MS Thermo Scientific Exactive MS. MS MS:1000649 Exactive Thermo Scientific Exactive MS. PSI:MS Thermo Scientific software for data analysis of peptides and proteins. MS MS:1000650 Proteome Discoverer Thermo Scientific software for data analysis of peptides and proteins. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200. MS MS:1000651 3200 QTRAP SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer. MS MS:1000652 4800 Plus MALDI TOF/TOF SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS. MS MS:1000653 API 3200 SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS. MS MS:1000654 API 5000 SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite. MS MS:1000655 QSTAR Elite SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite. PSI:MS Applied Biosystems|MDS SCIEX QSTAR Pulsar. MS MS:1000656 QSTAR Pulsar Applied Biosystems|MDS SCIEX QSTAR Pulsar. PSI:MS Applied Biosystems|MDS SCIEX QSTAR XL. MS MS:1000657 QSTAR XL Applied Biosystems|MDS SCIEX QSTAR XL. PSI:MS Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer. MS MS:1000658 4800 Proteomics Analyzer Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer. PSI:MS SCIEX or Applied Biosystems software for data acquisition and analysis. MS MS:1000659 4000 Series Explorer Software SCIEX or Applied Biosystems software for data acquisition and analysis. PSI:MS Waters Corporation Xevo MRT Mass Spectrometer. MS MS:1000660 Xevo MRT MS Waters Corporation Xevo MRT Mass Spectrometer. PSI:MS SCIEX or Applied Biosystems software for data acquisition and analysis. MS MS:1000661 GPS Explorer SCIEX or Applied Biosystems software for data acquisition and analysis. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification. MS MS:1000662 LightSight Software SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification. PSI:MS SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant. MS MS:1000663 ProteinPilot Software SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant. PSI:MS Applied Biosystems|MDS SCIEX software for tissue imaging. MS MS:1000664 TissueView Software Applied Biosystems|MDS SCIEX software for tissue imaging. PSI:MS Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling. MS MS:1000665 MarkerView Software Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling. PSI:MS Applied Biosystems|MDS SCIEX software for MRM assay development. MS MS:1000666 MRMPilot Software Applied Biosystems|MDS SCIEX software for MRM assay development. PSI:MS Applied Biosystems|MDS SCIEX software for bio-related data exploration. MS MS:1000667 BioAnalyst Applied Biosystems|MDS SCIEX software for bio-related data exploration. PSI:MS Applied Biosystems|MDS SCIEX software for protein identification. MS MS:1000668 Pro ID Applied Biosystems|MDS SCIEX software for protein identification. PSI:MS Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT. MS MS:1000669 Pro ICAT Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT. PSI:MS Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ. MS MS:1000670 Pro Quant Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ. PSI:MS Applied Biosystems|MDS SCIEX software for MS-BLAST identification. MS MS:1000671 Pro BLAST Applied Biosystems|MDS SCIEX software for MS-BLAST identification. PSI:MS SCIEX Cliquid software for data analysis and quantitation. MS MS:1000672 Cliquid SCIEX Cliquid software for data analysis and quantitation. PSI:MS Applied Biosystems|MDS SCIEX software for MRM assay development. MS MS:1000673 MIDAS Workflow Designer Applied Biosystems|MDS SCIEX software for MRM assay development. PSI:MS Applied Biosystems|MDS SCIEX software for MRM-based quantitation. MS MS:1000674 MultiQuant Applied Biosystems|MDS SCIEX software for MRM-based quantitation. PSI:MS The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. MS MS:1000675 6220 Time-of-Flight LC/MS The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. PSI:MS The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. MS MS:1000676 6510 Quadrupole Time-of-Flight LC/MS The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. PSI:MS The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. MS MS:1000677 6520A Quadrupole Time-of-Flight LC/MS The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. PSI:MS Software for data acquisition of 6000 series instruments. MS MS:1000678 MassHunter Data Acquisition Software for data acquisition of 6000 series instruments. PSI:MS Software for open access data acquisition. MS MS:1000679 MassHunter Easy Access Software for open access data acquisition. PSI:MS Software for data analysis of data from 6000 series instruments. MS MS:1000680 MassHunter Qualitative Analysis Software for data analysis of data from 6000 series instruments. PSI:MS Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data. MS MS:1000681 MassHunter Quantitative Analysis Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data. PSI:MS Software for identification of metabolites. MS MS:1000682 MassHunter Metabolite ID Software for identification of metabolites. PSI:MS Software for protein characterization. MS MS:1000683 MassHunter BioConfirm Software for protein characterization. PSI:MS Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. MS MS:1000684 Genespring MS Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. PSI:MS Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. MS MS:1000685 MassHunter Mass Profiler Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. PSI:MS Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites. MS MS:1000686 METLIN Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites. PSI:MS Software for protein identification and characterization of complex protein digest mixtures. MS MS:1000687 Spectrum Mill for MassHunter Workstation Software for protein identification and characterization of complex protein digest mixtures. PSI:MS Software for data analysis of 6300 series ion trap mass spectrometers. MS MS:1000688 6300 Series Ion Trap Data Analysis Software Software for data analysis of 6300 series ion trap mass spectrometers. PSI:MS Agilent software for data acquisition and analysis. MS MS:1000689 Agilent software Agilent software for data acquisition and analysis. PSI:MS SCIEX or Applied Biosystems software for data acquisition and analysis. MS MS:1000690 SCIEX software SCIEX or Applied Biosystems software for data acquisition and analysis. PSI:MS Applied Biosystems|MDS SCIEX software for data acquisition and analysis. MS MS:1000691 Applied Biosystems software Applied Biosystems|MDS SCIEX software for data acquisition and analysis. PSI:MS Bruker software for data acquisition and analysis. MS MS:1000692 Bruker software Bruker software for data acquisition and analysis. PSI:MS Thermo Finnigan software for data acquisition and analysis. MS Bioworks Browser MS:1000693 Thermo Finnigan software Thermo Finnigan software for data acquisition and analysis. PSI:MS Waters software for data acquisition and analysis. MS MS:1000694 Waters software Waters software for data acquisition and analysis. PSI:MS Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. MS MS:1000695 apex ultra Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. PSI:MS Bruker Daltonics' autoflex III smartbeam: MALDI TOF. MS MS:1000696 autoflex III smartbeam Bruker Daltonics' autoflex III smartbeam: MALDI TOF. PSI:MS Bruker Daltonics' HCT Series. MS MS:1000697 Bruker Daltonics HCT Series Bruker Daltonics' HCT Series. PSI:MS Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI. MS MS:1000698 HCTultra Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI. PSI:MS Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR. MS MS:1000699 HCTultra PTM Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR. PSI:MS Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD. MS MS:1000700 HCTultra ETD II Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD. PSI:MS Bruker Daltonics' microflex LT: MALDI TOF. MS MS:1000701 microflex LT Bruker Daltonics' microflex LT: MALDI TOF. PSI:MS Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI. MS MS:1000702 micrOTOF Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI. PSI:MS Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI. MS MS:1000703 micrOTOF-Q Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI. PSI:MS Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI. MS MS:1000704 micrOTOF-Q II Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI. PSI:MS Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF. MS MS:1000705 ultraflex III TOF/TOF Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF. PSI:MS Bruker software for data acquisition. MS MS:1000706 apexControl Bruker software for data acquisition. PSI:MS Bruker software for data analysis. MS MS:1000707 BioTools Bruker software for data analysis. PSI:MS Bruker CLINPROT software. MS MS:1000708 CLINPROT Bruker CLINPROT software. PSI:MS Bruker CLINPROT micro software. MS MS:1000709 CLINPROT micro Bruker CLINPROT micro software. PSI:MS Bruker CLINPROT robot software. MS MS:1000710 CLINPROT robot Bruker CLINPROT robot software. PSI:MS Bruker ClinProTools software. MS MS:1000711 ClinProTools Bruker ClinProTools software. PSI:MS Bruker Compass software. MS MS:1000712 Compass Bruker Compass software. PSI:MS Bruker Compass for HCT/esquire software. MS MS:1000713 Compass for HCT/esquire Bruker Compass for HCT/esquire software. PSI:MS Bruker Compass for micrOTOF software. MS MS:1000714 Compass for micrOTOF Bruker Compass for micrOTOF software. PSI:MS Bruker compass OpenAccess software. MS MS:1000715 Compass OpenAccess Bruker compass OpenAccess software. PSI:MS Bruker compass Security Pack software. MS MS:1000716 Compass Security Pack Bruker compass Security Pack software. PSI:MS Bruker stand-alone software for data conversion. MS MS:1000717 CompassXport Bruker stand-alone software for data conversion. PSI:MS Bruker software library for data access. MS MS:1000718 CompassXtract Bruker software library for data access. PSI:MS Bruker software for data analysis. MS MS:1000719 DataAnalysis Bruker software for data analysis. PSI:MS Bruker software for data acquisition. MS MS:1000720 dpControl Bruker software for data acquisition. PSI:MS Bruker software for data acquisition. MS MS:1000721 esquireControl Bruker software for data acquisition. PSI:MS Bruker software for data analysis. MS MS:1000722 flexImaging Bruker software for data analysis. PSI:MS Bruker GENOLINK software. MS MS:1000723 GENOLINK Bruker GENOLINK software. PSI:MS Bruker GenoTools software. MS MS:1000724 GenoTools Bruker GenoTools software. PSI:MS Bruker software for data acquisition. MS MS:1000725 HCTcontrol Bruker software for data acquisition. PSI:MS Bruker software for data acquisition. MS MS:1000726 micrOTOFcontrol Bruker software for data acquisition. PSI:MS Bruker PolyTools software. MS MS:1000727 PolyTools Bruker PolyTools software. PSI:MS Bruker software for data analysis. MS MS:1000728 ProfileAnalysis Bruker software for data analysis. PSI:MS Bruker PROTEINEER software. MS MS:1000729 PROTEINEER Bruker PROTEINEER software. PSI:PI Bruker PROTEINEER dp software. MS MS:1000730 PROTEINEER dp Bruker PROTEINEER dp software. PSI:PI Bruker PROTEINEER fc software. MS MS:1000731 PROTEINEER fc Bruker PROTEINEER fc software. PSI:PI Bruker PROTEINEER spII software. MS MS:1000732 PROTEINEER spII Bruker PROTEINEER spII software. PSI:PI Bruker PROTEINEER-LC software. MS MS:1000733 PROTEINEER-LC Bruker PROTEINEER-LC software. PSI:PI Bruker ProteinScape software. MS MS:1000734 ProteinScape Bruker ProteinScape software. PSI:PI BrukerPureDisk software. MS MS:1000735 PureDisk BrukerPureDisk software. PSI:MS Bruker software for data analysis. MS MS:1000736 QuantAnalysis Bruker software for data analysis. PSI:MS Bruker software for data acquisition. MS MS:1000737 spControl Bruker software for data acquisition. PSI:MS Bruker TargetAnalysis software. MS MS:1000738 TargetAnalysis Bruker TargetAnalysis software. PSI:MS Bruker WARP-LC software. MS MS:1000739 WARP-LC Bruker WARP-LC software. PSI:MS Parameter file used to configure the acquisition of raw data on the instrument. MS MS:1000740 parameter file Parameter file used to configure the acquisition of raw data on the instrument. PSI:MS Conversion to dta format. MS MS:1000741 Conversion to dta Conversion to dta format. PSI:MS Thermo Finnigan SRF file format. MS MS:1000742 Bioworks SRF format Thermo Finnigan SRF file format. PSI:MS Thermo Scientific TSQ Quantum Ultra AM. MS MS:1000743 TSQ Quantum Ultra AM Thermo Scientific TSQ Quantum Ultra AM. PSI:MS Mass-to-charge ratio of an selected ion. MS MS:1000744 selected ion m/z Mass-to-charge ratio of an selected ion. PSI:MS The correction of the spectrum scan times, as used e.g. in label-free proteomics. MS MS:1000745 retention time alignment The correction of the spectrum scan times, as used e.g. in label-free proteomics. PSI:MS The removal of very high intensity data points. MS MS:1000746 high intensity data point removal The removal of very high intensity data points. PSI:MS The time that a data processing action was finished. MS MS:1000747 completion time The time that a data processing action was finished. PSI:MS ThermoFinnigan SSQ 7000 MS. MS MS:1000748 SSQ 7000 ThermoFinnigan SSQ 7000 MS. PSI:MS ThermoFinnigan TSQ 7000 MS. MS MS:1000749 TSQ 7000 ThermoFinnigan TSQ 7000 MS. PSI:MS ThermoFinnigan TSQ MS. MS MS:1000750 TSQ ThermoFinnigan TSQ MS. PSI:MS Thermo Scientific TSQ Quantum Ultra. MS MS:1000751 TSQ Quantum Ultra Thermo Scientific TSQ Quantum Ultra. PSI:MS TOPP (The OpenMS proteomics pipeline) software. MS MS:1000752 TOPP software TOPP (The OpenMS proteomics pipeline) software. PSI:MS Removes the baseline from profile spectra using a top-hat filter. MS MS:1000753 BaselineFilter Removes the baseline from profile spectra using a top-hat filter. PSI:MS Exports data from an OpenMS database to a file. MS MS:1000754 DBExporter Exports data from an OpenMS database to a file. PSI:MS Imports data to an OpenMS database. MS MS:1000755 DBImporter Imports data to an OpenMS database. PSI:MS Converts between different MS file formats. MS MS:1000756 FileConverter Converts between different MS file formats. PSI:MS Extracts or manipulates portions of data from peak, feature or consensus feature files. MS MS:1000757 FileFilter Extracts or manipulates portions of data from peak, feature or consensus feature files. PSI:MS Merges several MS files into one file. MS MS:1000758 FileMerger Merges several MS files into one file. PSI:MS Applies an internal calibration. MS MS:1000759 InternalCalibration Applies an internal calibration. PSI:MS OBSOLETE Corrects retention time distortions between maps. MS MS:1000760 This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch. MapAligner true OBSOLETE Corrects retention time distortions between maps. PSI:MS Normalizes peak intensities in an MS run. MS MS:1000761 MapNormalizer Normalizes peak intensities in an MS run. PSI:MS OBSOLETE Removes noise from profile spectra by using different smoothing techniques. MS MS:1000762 This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch. NoiseFilter true OBSOLETE Removes noise from profile spectra by using different smoothing techniques. PSI:MS OBSOLETE Finds mass spectrometric peaks in profile mass spectra. MS MS:1000763 This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch. PeakPicker true OBSOLETE Finds mass spectrometric peaks in profile mass spectra. PSI:MS Transforms an LC/MS map into a resampled map or a png image. MS MS:1000764 Resampler Transforms an LC/MS map into a resampled map or a png image. PSI:MS OBSOLETE Applies a filter to peak spectra. MS MS:1000765 This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch. SpectraFilter true OBSOLETE Applies a filter to peak spectra. PSI:MS Applies time of flight calibration. MS MS:1000766 TOFCalibration Applies time of flight calibration. PSI:MS Describes how the native spectrum identifiers are formated. nativeID format MS MS:1000767 native spectrum identifier format Describes how the native spectrum identifiers are formated. PSI:MS Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger. MS MS:1000768 Thermo nativeID format Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger. PSI:MS Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. MS MS:1000769 Waters nativeID format Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. PSI:MS Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger. MS MS:1000770 WIFF nativeID format Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger. PSI:MS Native format defined by scan=xsd:nonNegativeInteger. MS MS:1000771 Bruker/Agilent YEP nativeID format Native format defined by scan=xsd:nonNegativeInteger. PSI:MS Native format defined by scan=xsd:nonNegativeInteger. MS MS:1000772 Bruker BAF nativeID format Native format defined by scan=xsd:nonNegativeInteger. PSI:MS Native format defined by file=xsd:IDREF. MS MS:1000773 The nativeID must be the same as the source file ID. Bruker FID nativeID format Native format defined by file=xsd:IDREF. PSI:MS Native format defined by index=xsd:nonNegativeInteger. MS MS:1000774 Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. multiple peak list nativeID format Native format defined by index=xsd:nonNegativeInteger. PSI:MS Native format defined by file=xsd:IDREF. MS MS:1000775 The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. single peak list nativeID format Native format defined by file=xsd:IDREF. PSI:MS Native format defined by scan=xsd:nonNegativeInteger. MS MS:1000776 Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. scan number only nativeID format Native format defined by scan=xsd:nonNegativeInteger. PSI:MS Native format defined by spectrum=xsd:nonNegativeInteger. MS MS:1000777 Used for conversion from mzData. The spectrum id attribute is referenced. spectrum identifier nativeID format Native format defined by spectrum=xsd:nonNegativeInteger. PSI:MS A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm. MS MS:1000778 charge state calculation A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm. PSI:MS Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z. MS MS:1000779 below precursor intensity dominance charge state calculation Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z. PSI:MS A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions. MS MS:1000780 precursor recalculation A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions. PSI:MS Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans. MS MS:1000781 msPrefix precursor recalculation Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans. PSI:MS Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques. MS MS:1000782 Savitzky-Golay smoothing Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques. PSI:MS Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible. MS MS:1000783 LOWESS smoothing Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible. PSI:MS Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function. Weierstrass transform binomial smoothing MS MS:1000784 Gaussian smoothing Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function. PSI:MS Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect. box smoothing boxcar smoothing sliding average smoothing MS MS:1000785 moving average smoothing Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect. PSI:MS A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added. binary-data-type:MS:1000519 binary-data-type:MS:1000521 binary-data-type:MS:1000522 binary-data-type:MS:1000523 binary-data-type:MS:1001479 MS MS:1000786 non-standard data array A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added. PSI:MS binary-data-type:MS:1000519 32-bit integer binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000522 64-bit integer binary-data-type:MS:1000523 64-bit float binary-data-type:MS:1001479 null-terminated ASCII string Threshold at or below which some action is taken. MS MS:1000787 inclusive low intensity threshold Threshold at or below which some action is taken. PSI:MS Threshold at or above which some action is taken. MS MS:1000788 inclusive high intensity threshold Threshold at or above which some action is taken. PSI:MS MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions. MS MS:1000789 enhanced multiply charged spectrum MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions. PSI:MS MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation. MS MS:1000790 time-delayed fragmentation spectrum MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation. PSI:MS OBSOLETE Scan with enhanced resolution. MS MS:1000791 This term was made obsolete because it was merged with zoom scan (MS:1000497). enhanced resolution scan true OBSOLETE Scan with enhanced resolution. PSI:MS Isolation window parameter. MS MS:1000792 isolation window attribute Isolation window parameter. PSI:MS OBSOLETE The highest m/z being isolated in an isolation window. MS MS:1000793 This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. isolation window upper limit true OBSOLETE The highest m/z being isolated in an isolation window. PSI:MS OBSOLETE The lowest m/z being isolated in an isolation window. MS MS:1000794 This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. isolation window lower limit true OBSOLETE The lowest m/z being isolated in an isolation window. PSI:MS Use this term if only one scan was recorded or there is no information about scans available. MS MS:1000795 no combination Use this term if only one scan was recorded or there is no information about scans available. PSI:MS Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file. MS MS:1000796 This is the preferred storage place for the spectrum TITLE from an MGF peak list. spectrum title Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file. PSI:MS A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. MS MS:1000797 This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. peak list scans A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. PSI:MS A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. MS MS:1000798 This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. peak list raw scans A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. PSI:MS A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added. MS MS:1000799 custom unreleased software tool A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added. PSI:MS The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported. MS MS:1000800 mass resolving power The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported. PSI:MS Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported. sum peak picking MS MS:1000801 area peak picking Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported. PSI:MS Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported. max peak picking MS MS:1000802 height peak picking Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported. PSI:MS Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value. MS MS:1000803 analyzer scan offset Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value. PSI:MS A plot of the relative intensity of electromagnetic radiation as a function of the wavelength. EMR spectrum MS MS:1000804 electromagnetic radiation spectrum A plot of the relative intensity of electromagnetic radiation as a function of the wavelength. PSI:MS A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited. MS MS:1000805 emission spectrum A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited. PSI:MS A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited. MS MS:1000806 absorption spectrum A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited. PSI:MS Unit describing the scan rate of a spectrum in Thomson per second. MS MS:1000807 Th/s Unit describing the scan rate of a spectrum in Thomson per second. PSI:MS Chromatogram properties that are associated with a value. MS MS:1000808 chromatogram attribute Chromatogram properties that are associated with a value. PSI:MS A free-form text title describing a chromatogram. MS MS:1000809 This is the preferred storage place for the spectrum title. chromatogram title A free-form text title describing a chromatogram. PSI:MS Representation of the current of ions versus time. MS MS:1000810 ion current chromatogram Representation of the current of ions versus time. PSI:MS Representation of electromagnetic properties versus time. EMR radiation chromatogram MS MS:1000811 electromagnetic radiation chromatogram Representation of electromagnetic properties versus time. PSI:MS Representation of light absorbed by the sample versus time. MS MS:1000812 absorption chromatogram Representation of light absorbed by the sample versus time. PSI:MS Representation of light emitted by the sample versus time. MS MS:1000813 emission chromatogram Representation of light emitted by the sample versus time. PSI:MS The number of counted events observed per second in one or a group of elements of a detector. MS MS:1000814 counts per second The number of counted events observed per second in one or a group of elements of a detector. PSI:MS Bruker BAF raw file format. MS MS:1000815 Bruker BAF format Bruker BAF raw file format. PSI:MS Bruker HyStar U2 file format. MS MS:1000816 Bruker U2 format Bruker HyStar U2 file format. PSI:MS Bruker software for hyphenated experiments. MS MS:1000817 HyStar Bruker software for hyphenated experiments. PSI:MS Acquity UPLC Photodiode Array Detector. MS MS:1000818 Acquity UPLC PDA Acquity UPLC Photodiode Array Detector. PSI:MS Acquity UPLC Fluorescence Detector. MS MS:1000819 Acquity UPLC FLR Acquity UPLC Fluorescence Detector. PSI:MS A data array of flow rate measurements. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000820 flow rate array A data array of flow rate measurements. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of pressure measurements. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000821 pressure array A data array of pressure measurements. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of temperature measurements. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1000822 temperature array A data array of temperature measurements. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. MS MS:1000823 Bruker U2 nativeID format Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. PSI:MS No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format. MS MS:1000824 no nativeID format No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format. PSI:MS Bruker FID file format. MS MS:1000825 Bruker FID format Bruker FID file format. PSI:MS The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography. MS MS:1000826 elution time The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography. PSI:MS The primary or reference m/z about which the isolation window is defined. MS MS:1000827 isolation window target m/z The primary or reference m/z about which the isolation window is defined. PSI:MS The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. MS MS:1000828 isolation window lower offset The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. PSI:MS The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. MS MS:1000829 isolation window upper offset The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. PSI:MS Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation. MS MS:1000830 See MS:1000014 for the related term of accuracy. precision Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation. PSI:MS Properties of the preparation steps which took place before the measurement was performed. MS MS:1000831 sample preparation Properties of the preparation steps which took place before the measurement was performed. PSI:MS Attributes to describe the technique how the sample is prepared with the matrix solution. MS MS:1000832 MALDI matrix application Attributes to describe the technique how the sample is prepared with the matrix solution. PSI:MS Describes the technique how the matrix is put on the sample target. MS MS:1000833 matrix application type Describes the technique how the matrix is put on the sample target. PSI:MS Describes the chemical solution used as matrix. MS MS:1000834 matrix solution Describes the chemical solution used as matrix. PSI:MS Concentration of the chemical solution used as matrix. MS MS:1000835 matrix solution concentration Concentration of the chemical solution used as matrix. PSI:MS Dried droplet in MALDI matrix preparation. MS MS:1000836 dried droplet MALDI matrix preparation Dried droplet in MALDI matrix preparation. PSI:MS Printed MALDI matrix preparation. MS MS:1000837 printed MALDI matrix preparation Printed MALDI matrix preparation. PSI:MS Sprayed MALDI matrix preparation. MS MS:1000838 sprayed MALDI matrix preparation Sprayed MALDI matrix preparation. PSI:MS Precoated MALDI sample plate. MS MS:1000839 precoated MALDI sample plate Precoated MALDI sample plate. PSI:MS Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation. MS MS:1000840 laser Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation. PSI:MS Laser properties that are associated with a value. MS MS:1000841 laser attribute Laser properties that are associated with a value. PSI:MS Type of laser used for desorption purpose. MS MS:1000842 laser type Type of laser used for desorption purpose. PSI:MS OBSOLETE The distance between two peaks of the emitted laser beam. MS MS:1000843 This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242). wavelength true OBSOLETE The distance between two peaks of the emitted laser beam. PSI:MS Describes the diameter of the laser beam in x direction. MS MS:1000844 focus diameter x Describes the diameter of the laser beam in x direction. PSI:MS Describes the diameter of the laser beam in y direction. MS MS:1000845 focus diameter y Describes the diameter of the laser beam in y direction. PSI:MS Describes output energy of the laser system. May be attenuated by filters or other means. MS MS:1000846 pulse energy Describes output energy of the laser system. May be attenuated by filters or other means. PSI:MS Describes how long the laser beam was emitted from the laser device. MS MS:1000847 pulse duration Describes how long the laser beam was emitted from the laser device. PSI:MS Describes the reduction of the intensity of the laser beam energy. MS MS:1000848 attenuation Describes the reduction of the intensity of the laser beam energy. PSI:MS Describes the angle between the laser beam and the sample target. MS MS:1000849 impact angle Describes the angle between the laser beam and the sample target. PSI:MS Laser which is powered by a gaseous medium. MS MS:1000850 gas laser Laser which is powered by a gaseous medium. PSI:MS Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states. MS MS:1000851 solid-state laser Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states. PSI:MS Dye lasers use an organic dye as the gain medium. MS MS:1000852 dye-laser Dye lasers use an organic dye as the gain medium. PSI:MS Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term. MS MS:1000853 free electron laser Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term. PSI:MS Thermo Scientific LTQ XL MS. MS MS:1000854 LTQ XL Thermo Scientific LTQ XL MS. PSI:MS Thermo Scientific LTQ Velos MS. MS MS:1000855 LTQ Velos Thermo Scientific LTQ Velos MS. PSI:MS Thermo Scientific LTQ Velos MS with ETD. MS MS:1000856 LTQ Velos ETD Thermo Scientific LTQ Velos MS with ETD. PSI:MS Properties of the described run. MS MS:1000857 run attribute Properties of the described run. PSI:MS Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information. MS MS:1000858 fraction identifier Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information. PSI:MS Group of two or more atoms held together by chemical bonds. MS MS:1000859 molecule Group of two or more atoms held together by chemical bonds. https://en.wikipedia.org/wiki/Molecule A molecule of low molecular weight that is composed of two or more amino acid residues. MS MS:1000860 peptide A molecule of low molecular weight that is composed of two or more amino acid residues. PSI:MS A physical characteristic of a molecular entity. MS MS:1000861 molecular entity property A physical characteristic of a molecular entity. PSI:MS The pH of a solution at which a charged molecule does not migrate in an electric field. pI MS MS:1000862 isoelectric point The pH of a solution at which a charged molecule does not migrate in an electric field. PSI:MS The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm. predicted pI MS MS:1000863 predicted isoelectric point The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm. PSI:MS A combination of symbols used to express the chemical composition of a molecule. MS MS:1000864 chemical formula A combination of symbols used to express the chemical composition of a molecule. EDAM:0846 A chemical formula which expresses the proportions of the elements present in a substance. MS MS:1000865 empirical formula A chemical formula which expresses the proportions of the elements present in a substance. PSI:MS A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked. MS MS:1000866 molecular formula A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked. PSI:MS A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. MS MS:1000867 structural formula A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. PSI:MS The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. MS MS:1000868 SMILES string The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. EDAM:2301 The gas pressure of the collision gas used for collisional excitation. MS MS:1000869 collision gas pressure The gas pressure of the collision gas used for collisional excitation. PSI:MS OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000. MS MS:1000870 This term was obsoleted because was redundant to MS:1000139. 4000 QTRAP true OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000. PSI:MS Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs. MS MS:1000871 SRM software Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs. PSI:MS Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. MS MS:1000872 MaRiMba Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba Software used to predict or calculate numerical attributes of peptides. MS MS:1000873 peptide attribute calculation software Software used to predict or calculate numerical attributes of peptides. PSI:MS Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence. MS MS:1000874 SSRCalc Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence. http://hs2.proteome.ca/SSRCalc/SSRCalc.html Potential difference between the orifice and the skimmer in volts. MS MS:1000875 declustering potential Potential difference between the orifice and the skimmer in volts. PSI:MS Potential difference between the sampling cone/orifice in volts. MS MS:1000876 cone voltage Potential difference between the sampling cone/orifice in volts. PSI:MS Potential difference setting of the tube lens in volts. MS MS:1000877 tube lens voltage Potential difference setting of the tube lens in volts. PSI:MS An identifier/accession number to an external reference database. MS MS:1000878 external reference identifier An identifier/accession number to an external reference database. PSI:MS A unique identifier for a publication in the PubMed database (MIR:00000015). MS MS:1000879 PubMed identifier A unique identifier for a publication in the PubMed database (MIR:00000015). PSI:MS The duration of intervals between scanning, during which the instrument configuration is switched. MS MS:1000880 interchannel delay The duration of intervals between scanning, during which the instrument configuration is switched. PSI:MS Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. MS MS:1000881 molecular entity Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. https://en.wikipedia.org/wiki/Molecular_entity A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene. MS MS:1000882 protein A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene. PSI:MS A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN). MS MS:1000883 protein short name A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN). PSI:MS An nonphysical characterstic attributed to a specific protein. MS MS:1000884 protein attribute An nonphysical characterstic attributed to a specific protein. PSI:MS Identifier for a specific protein in a database. MS MS:1000885 protein accession Identifier for a specific protein in a database. PSI:MS A long name describing the function of the protein. MS MS:1000886 protein name A long name describing the function of the protein. PSI:MS Nonphysical characteristic attributed to a peptide. MS MS:1000887 peptide attribute Nonphysical characteristic attributed to a peptide. PSI:MS Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away. MS MS:1000888 stripped peptide sequence Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away. PSI:MS Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present. MS MS:1000889 Make it more general as there are actually many other ways to display a modified peptide sequence. peptidoform sequence Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present. PSI:MS A state description of how a peptide might be isotopically or isobarically labelled. MS MS:1000890 peptidoform labeling state A state description of how a peptide might be isotopically or isobarically labelled. PSI:MS A peptide that has been created or labelled with some heavier-than-usual isotopes. MS MS:1000891 heavy labeled peptidoform A peptide that has been created or labelled with some heavier-than-usual isotopes. PSI:MS A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy". light labeled peptide MS MS:1000892 unlabeled peptidoform A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy". PSI:MS An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. MS MS:1000893 peptidoform group label An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. PSI:MS A time interval from the start of chromatography when an analyte exits a chromatographic column. MS MS:1000894 retention time A time interval from the start of chromatography when an analyte exits a chromatographic column. PSI:MS A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup. MS MS:1000895 local retention time A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup. PSI:MS A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup. MS MS:1000896 normalized retention time A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup. PSI:MS A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application. MS MS:1000897 predicted retention time A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application. PSI:MS Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. MS MS:1000898 standard Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. PSI:MS A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. MS MS:1000899 de facto standard A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. PSI:MS A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. MS MS:1000900 minimum information standard A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. PSI:MS A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column. MS MS:1000901 retention time normalization standard A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column. PSI:MS The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column. MS MS:1000902 H-PINS retention time normalization standard The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column. DOI:10.1074/mcp.M800569-MCP200 PMID:19411281 The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion). MS MS:1000903 product ion series ordinal The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion). PSI:PI The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z. MS MS:1000904 product ion m/z delta The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z. PSI:PI The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries. MS MS:1000905 percent of base peak times 100 The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries. PSI:MS Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc. MS MS:1000906 peak intensity rank Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc. PSI:MS Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant. MS MS:1000907 peak targeting suitability rank Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant. PSI:MS A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely. reaction MS MS:1000908 transition A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely. PSI:MS The strategy used to validate that a transition is effective. MS MS:1000909 transition validation method The strategy used to validate that a transition is effective. PSI:MS The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined. MS MS:1000910 transition optimized on specified instrument The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined. PSI:MS The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. MS MS:1000911 transition validated with an MS/MS spectrum on specified instrument The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. PSI:MS The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad). MS MS:1000912 transition purported from an MS/MS spectrum on a different, specified instrument The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad). PSI:MS The transition has been predicted by informatics software without any direct spectral evidence. MS MS:1000913 transition predicted by informatic analysis The transition has been predicted by informatics software without any direct spectral evidence. PSI:MS A file format that has two or more columns of tabular data where each column is separated by a TAB character. MS MS:1000914 tab delimited text format A file format that has two or more columns of tabular data where each column is separated by a TAB character. PSI:MS An attribute of a window in time about which a peptide might elute from the column. MS MS:1000915 retention time window attribute An attribute of a window in time about which a peptide might elute from the column. PSI:MS The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time. MS MS:1000916 retention time window lower offset The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time. PSI:MS The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time. MS MS:1000917 retention time window upper offset The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time. PSI:MS A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically. MS MS:1000918 target list A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically. PSI:MS A priority setting specifying whether included or excluded targets have priority over the other. MS MS:1000919 target inclusion exclusion priority A priority setting specifying whether included or excluded targets have priority over the other. PSI:MS A priority setting specifying that included targets have priority over the excluded targets if there is a conflict. MS MS:1000920 includes supersede excludes A priority setting specifying that included targets have priority over the excluded targets if there is a conflict. PSI:MS A priority setting specifying that excluded targets have priority over the included targets if there is a conflict. MS MS:1000921 excludes supersede includes A priority setting specifying that excluded targets have priority over the included targets if there is a conflict. PSI:MS Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington. MS MS:1000922 Skyline Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington. https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology. MS MS:1000923 TIQAM Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology. http://tools.proteomecenter.org/TIQAM/TIQAM.html OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. MS:1000872 MS MS:1000924 This term was made obsolete because it was redundant with an existing term (MS:1000872). MaRiMba true OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology. MS MS:1000925 ATAQS Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology. PSI:MS The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1. MS MS:1000926 product interpretation rank The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1. PSI:MS The length of time spent filling an ion trapping device. MS MS:1000927 ion injection time The length of time spent filling an ion trapping device. PSI:MS A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample. MS MS:1000928 calibration spectrum A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample. PSI:MS Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger. MS MS:1000929 Shimadzu Biotech nativeID format Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger. PSI:MS Shimadzu Biotech format. MS MS:1000930 Shimadzu Biotech database entity Shimadzu Biotech format. PSI:MS Applied Biosystems|MDS SCIEX QTRAP 5500. MS MS:1000931 QTRAP 5500 Applied Biosystems|MDS SCIEX QTRAP 5500. PSI:MS SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer. MS MS:1000932 TripleTOF 5600 SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer. PSI:MS Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation. MS MS:1000933 protein modifications Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation. PSI:MS Name of the gene from which the protein is translated. MS MS:1000934 gene name Name of the gene from which the protein is translated. PSI:MS The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1000935 6470A Triple Quadrupole LC/MS The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1000936 6470B Triple Quadrupole LC/MS The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1000937 6495C Triple Quadrupole LC/MS The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra. MS MS:1001000 spectrum interpretation Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra. PSI:PI MS MS:1001005 SEQUEST:CleavesAt SEQUEST View Input Parameters. MS MS:1001006 SEQUEST:ViewCV SEQUEST View Input Parameters. PSI:PI Number of peptide results to show. MS MS:1001007 SEQUEST:OutputLines Number of peptide results to show. PSI:MS Number of full protein descriptions to show for top N peptides. MS MS:1001009 SEQUEST:DescriptionLines Number of full protein descriptions to show for top N peptides. PSI:MS A de novo sequencing search (without database). MS MS:1001010 de novo search A de novo sequencing search (without database). PSI:PI Details about the database searched. MS MS:1001011 search database details Details about the database searched. PSI:PI The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other). MS MS:1001012 database source The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other). PSI:PI The name of the search database (nr, SwissProt or est_human). MS MS:1001013 database name The name of the search database (nr, SwissProt or est_human). PSI:PI OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view. MS MS:1001014 database local file path true OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view. PSI:PI URI, from where the search database was originally downloaded. MS MS:1001015 database original uri URI, from where the search database was originally downloaded. PSI:PI Version of the search database. In mzIdentML use the attribute instead. MS MS:1001016 database version Version of the search database. In mzIdentML use the attribute instead. PSI:PI Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term. MS MS:1001017 release date Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term. PSI:PI Database containing amino acid or nucleic acid sequences. MS MS:1001018 database type Database containing amino acid or nucleic acid sequences. PSI:PI Was there filtering used on the database. MS MS:1001019 database filtering Was there filtering used on the database. PSI:PI A taxonomy filter was to the database search. MS MS:1001020 DB filter taxonomy A taxonomy filter was to the database search. PSI:PI Filtering applied specifically by accession number pattern. MS MS:1001021 DB filter on accession numbers Filtering applied specifically by accession number pattern. PSI:PI Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value. MS MS:1001022 DB MW filter Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value. PSI:PI Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value. MS MS:1001023 DB PI filter Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value. PSI:PI The translated open reading frames from a nucleotide database considered in the search (range: 1-6). MS MS:1001024 translation frame The translated open reading frames from a nucleotide database considered in the search (range: 1-6). PSI:PI The translation table used to translate the nucleotides to amino acids. MS MS:1001025 translation table The translation table used to translate the nucleotides to amino acids. PSI:PI MS MS:1001026 SEQUEST:NormalizeXCorrValues Filtering applied specifically by amino acid sequence pattern. MS MS:1001027 DB filter on sequence pattern Filtering applied specifically by amino acid sequence pattern. PSI:PI String in the header of a sequence entry for that entry to be searched. MS MS:1001028 SEQUEST:SequenceHeaderFilter String in the header of a sequence entry for that entry to be searched. PSI:MS The number of sequences (proteins / nucleotides) from the database search after filtering. MS MS:1001029 number of sequences searched The number of sequences (proteins / nucleotides) from the database search after filtering. PSI:PI Number of peptide seqs compared to each spectrum. MS MS:1001030 number of peptide seqs compared to each spectrum Number of peptide seqs compared to each spectrum. PSI:PI A search using a library of spectra. MS MS:1001031 spectral library search A search using a library of spectra. PSI:PI MS MS:1001032 SEQUEST:SequencePartialFilter OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run. MS MS:1001035 date / time search performed true OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run. PSI:PI The time taken to complete the search in seconds. MS MS:1001036 search time taken The time taken to complete the search in seconds. PSI:PI Flag indicating that fragment ions should be shown. MS MS:1001037 SEQUEST:ShowFragmentIons Flag indicating that fragment ions should be shown. PSI:MS Specify depth as value of the CVParam. MS MS:1001038 SEQUEST:Consensus Specify depth as value of the CVParam. PSI:PI Type of the source file, the mzIdentML was created from. MS MS:1001040 intermediate analysis format Type of the source file, the mzIdentML was created from. PSI:PI SEQUEST View / Sort Input Parameters. MS MS:1001041 SEQUEST:sortCV SEQUEST View / Sort Input Parameters. PSI:PI Specify "number of dtas shown" as value of the CVParam. MS MS:1001042 SEQUEST:LimitTo Specify "number of dtas shown" as value of the CVParam. PSI:PI Details of cleavage agent (enzyme). MS MS:1001044 cleavage agent details Details of cleavage agent (enzyme). PSI:PI The name of the cleavage agent. MS MS:1001045 cleavage agent name The name of the cleavage agent. PSI:PI Sort order of SEQUEST search results by the delta of the normalized correlation score. MS MS:1001046 SEQUEST:sort by dCn Sort order of SEQUEST search results by the delta of the normalized correlation score. PSI:PI Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M. MS MS:1001047 SEQUEST:sort by dM Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M. PSI:PI Sort order of SEQUEST search results given by the ions. MS MS:1001048 SEQUEST:sort by Ions Sort order of SEQUEST search results given by the ions. PSI:PI Sort order of SEQUEST search results given by the mass of the protonated ion. MS MS:1001049 SEQUEST:sort by MH+ Sort order of SEQUEST search results given by the mass of the protonated ion. PSI:PI Sort order of SEQUEST search results given by the probability. MS MS:1001050 SEQUEST:sort by P Sort order of SEQUEST search results given by the probability. PSI:PI OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any. MS MS:1001051 multiple enzyme combination rules true OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any. PSI:PI Sort order of SEQUEST search results given by the previous amino acid. MS MS:1001052 SEQUEST:sort by PreviousAminoAcid Sort order of SEQUEST search results given by the previous amino acid. PSI:PI Sort order of SEQUEST search results given by the reference. MS MS:1001053 SEQUEST:sort by Ref Sort order of SEQUEST search results given by the reference. PSI:PI Modification parameters for the search engine run. MS MS:1001055 modification parameters Modification parameters for the search engine run. PSI:PI The specificity rules for the modifications applied by the search engine. MS MS:1001056 modification specificity rule The specificity rules for the modifications applied by the search engine. PSI:PI OBSOLETE: Tolerance on types. MS MS:1001057 tolerance on types true OBSOLETE: Tolerance on types. PSI:PI The quality estimation was done manually. MS MS:1001058 quality estimation by manual validation The quality estimation was done manually. PSI:PI Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide). MS MS:1001059 SEQUEST:sort by RSp Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide). PSI:PI Method for quality estimation (manually or with decoy database). MS MS:1001060 quality estimation method details Method for quality estimation (manually or with decoy database). PSI:PI OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD. MS:1000336 MS MS:1001061 neutral loss true OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD. PSI:PI Mascot MGF file format. MS MS:1001062 Mascot MGF format Mascot MGF file format. PSI:MS OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms. MS:1001961 MS MS:1001065 This term was made obsolete and is replaced by the term (MS:1001961). TODOscoring model true OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms. PSI:PI The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine. MS MS:1001066 ions series considered in search The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine. PSI:PI Sort order of SEQUEST search results by the Sp score. MS MS:1001068 SEQUEST:sort by Sp Sort order of SEQUEST search results by the Sp score. PSI:PI Sort order of SEQUEST search results given by the total ion current. MS MS:1001069 SEQUEST:sort by TIC Sort order of SEQUEST search results given by the total ion current. PSI:PI Sort order of SEQUEST search results given by the scan number. MS MS:1001070 SEQUEST:sort by Scan Sort order of SEQUEST search results given by the scan number. PSI:PI Sort order of SEQUEST search results given by the sequence. MS MS:1001071 SEQUEST:sort by Sequence Sort order of SEQUEST search results given by the sequence. PSI:PI Sort order of SEQUEST search results given by the SEQUEST result 'Sf'. MS MS:1001072 SEQUEST:sort by Sf Sort order of SEQUEST search results given by the SEQUEST result 'Sf'. PSI:PI Database contains amino acid sequences. MS MS:1001073 database type amino acid Database contains amino acid sequences. PSI:PI Database contains nucleic acid sequences. MS MS:1001079 database type nucleotide Database contains nucleic acid sequences. PSI:PI Enumeration of type of search value (i.e. from PMF, sequence tag, MS2). MS MS:1001080 search type Enumeration of type of search value (i.e. from PMF, sequence tag, MS2). PSI:PI A peptide mass fingerprint search. MS MS:1001081 pmf search A peptide mass fingerprint search. PSI:PI A sequence tag search. MS MS:1001082 tag search A sequence tag search. PSI:PI An MS2 search (with fragment ions). MS MS:1001083 ms-ms search An MS2 search (with fragment ions). PSI:PI Non-redundant GenBank sequence database. MS MS:1001084 database nr Non-redundant GenBank sequence database. PSI:PI Protein level information. MS MS:1001085 protein-level identification attribute Protein level information. PSI:PI Sort order of SEQUEST search results by the correlation score. MS MS:1001086 SEQUEST:sort by XCorr Sort order of SEQUEST search results by the correlation score. PSI:PI SEQUEST View / Process Input Parameters. MS MS:1001087 SEQUEST:ProcessCV SEQUEST View / Process Input Parameters. PSI:PI The protein description line from the sequence entry in the source database FASTA file. MS MS:1001088 protein description The protein description line from the sequence entry in the source database FASTA file. PSI:PI The taxonomy of the resultant molecule from the search. MS MS:1001089 molecule taxonomy The taxonomy of the resultant molecule from the search. PSI:PI OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT). MS:1001467 MS:1001468 MS:1001469 MS:1001470 MS MS:1001090 taxonomy nomenclature true OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT). PSI:PI MS MS:1001091 This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956). NoEnzyme true Identification confidence metric for a peptide. MS MS:1001092 peptide sequence-level identification statistic Identification confidence metric for a peptide. PSI:PI The percent coverage for the protein based upon the matched peptide sequences (can be calculated). MS MS:1001093 sequence coverage The percent coverage for the protein based upon the matched peptide sequences (can be calculated). PSI:PI Sort order of SEQUEST search results given by the charge. MS MS:1001094 SEQUEST:sort by z Sort order of SEQUEST search results given by the charge. PSI:PI MS MS:1001095 SEQUEST:ProcessAll Specify "percentage" as value of the CVParam. MS MS:1001096 SEQUEST:TopPercentMostIntense Specify "percentage" as value of the CVParam. PSI:PI This counts distinct sequences hitting the protein without regard to a minimal confidence threshold. MS MS:1001097 distinct peptide sequences This counts distinct sequences hitting the protein without regard to a minimal confidence threshold. PSI:PI This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere. MS MS:1001098 confident distinct peptide sequences This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere. PSI:PI The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than. MS MS:1001099 confident peptide qualification The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than. PSI:PI This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere. MS MS:1001100 confident peptide sequence number This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere. PSI:PI Protein group or subset relationships. MS MS:1001101 protein group or subset relationship Protein group or subset relationships. PSI:PI MS MS:1001102 SEQUEST:Chromatogram MS MS:1001103 SEQUEST:InfoAndLog The name of the UniProtKB/Swiss-Prot knowledgebase. MS MS:1001104 database UniProtKB/Swiss-Prot The name of the UniProtKB/Swiss-Prot knowledgebase. PSI:PI Peptide level information. MS MS:1001105 peptide sequence-level identification attribute Peptide level information. PSI:PI Specify "number" as value of the CVParam. MS MS:1001106 SEQUEST:TopNumber Specify "number" as value of the CVParam. PSI:PI Source file for this mzIdentML was a data set in a database. MS MS:1001107 data stored in database Source file for this mzIdentML was a data set in a database. PSI:PI Parameter information, type of product: a ion with charge on the N-terminal side. MS MS:1001108 param: a ion Parameter information, type of product: a ion with charge on the N-terminal side. PSI:PI Specify cull string as value of the CVParam. MS MS:1001109 SEQUEST:CullTo Specify cull string as value of the CVParam. PSI:PI SEQUEST Mode Input Parameters. MS MS:1001110 SEQUEST:modeCV SEQUEST Mode Input Parameters. PSI:PI MS MS:1001111 SEQUEST:Full Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein. MS MS:1001112 n-terminal flanking residue Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein. PSI:PI Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein. MS MS:1001113 c-terminal flanking residue Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein. PSI:PI OBSOLETE Retention time of the spectrum from the source file. MS MS:1001114 This term was made obsolete because scan start time (MS:1000016) should be used instead. retention time(s) true OBSOLETE Retention time of the spectrum from the source file. PSI:PI OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData. MS MS:1001115 This former purgatory term was made obsolete. scan number(s) true OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData. PSI:PI Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group). MS MS:1001116 single protein identification statistic Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group). PSI:PI The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier. theoretical mass MS MS:1001117 theoretical neutral mass The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier. PSI:PI Parameter information, type of product: b ion with charge on the N-terminal side. MS MS:1001118 param: b ion Parameter information, type of product: b ion with charge on the N-terminal side. PSI:PI Parameter information, type of product: c ion with charge on the N-terminal side. MS MS:1001119 param: c ion Parameter information, type of product: c ion with charge on the N-terminal side. PSI:PI MS MS:1001120 SEQUEST:FormatAndLinks The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count. MS MS:1001121 number of matched peaks The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count. PSI:PI The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb). MS MS:1001122 ions series considered The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb). PSI:PI The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't. MS MS:1001123 number of peaks used The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't. PSI:PI The number of peaks from the original peaks listed that were submitted to the search engine. MS MS:1001124 number of peaks submitted The number of peaks from the original peaks listed that were submitted to the search engine. PSI:PI Result of quality estimation: decision of a manual validation. MS MS:1001125 manual validation Result of quality estimation: decision of a manual validation. PSI:PI MS MS:1001126 SEQUEST:Fast Accessions Containing Sequence - Accessions for each protein containing this peptide. MS MS:1001127 peptide sharing details Accessions Containing Sequence - Accessions for each protein containing this peptide. PSI:PI SEQUEST Select Input Parameters. MS MS:1001128 SEQUEST:selectCV SEQUEST Select Input Parameters. PSI:PI Quantification information. MS MS:1001129 quantification information Quantification information. PSI:PI OBSOLETE Peptide raw area. MS MS:1001130 This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). peptide raw area true OBSOLETE Peptide raw area. PSI:PI Error on peptide area. MS MS:1001131 error on peptide area Error on peptide area. PSI:PI Peptide ratio. MS MS:1001132 peptide ratio Peptide ratio. PSI:PI Error on peptide ratio. MS MS:1001133 error on peptide ratio Error on peptide ratio. PSI:PI Protein ratio. MS MS:1001134 protein ratio Protein ratio. PSI:PI Error on protein ratio. MS MS:1001135 error on protein ratio Error on protein ratio. PSI:PI OBSOLETE P-value (protein diff from 1 randomly). MS MS:1001136 This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). p-value (protein diff from 1 randomly) true OBSOLETE P-value (protein diff from 1 randomly). PSI:PI Absolute quantity in terms of real concentration or molecule copy number in sample. MS MS:1001137 absolute quantity Absolute quantity in terms of real concentration or molecule copy number in sample. PSI:PI Error on absolute quantity. MS MS:1001138 error on absolute quantity Error on absolute quantity. PSI:PI Quantitation software name. MS MS:1001139 quantitation software name Quantitation software name. PSI:PI OBSOLETE Quantitation software version. MS MS:1001140 This term was made obsolete because part of mzQuantML schema. quantitation software version true OBSOLETE Quantitation software version. PSI:PI The intensity of the precursor ion. MS MS:1001141 intensity of precursor ion The intensity of the precursor ion. PSI:PI International Protein Index database for Homo sapiens sequences. MS MS:1001142 database IPI_human International Protein Index database for Homo sapiens sequences. PSI:PI Search engine specific peptide spectrum match scores. MS MS:1001143 PSM-level search engine specific statistic Search engine specific peptide spectrum match scores. PSI:PI MS MS:1001144 SEQUEST:SelectDefault SEQUEST Select Advanced Input Parameters. MS MS:1001145 SEQUEST:SelectAdvancedCV SEQUEST Select Advanced Input Parameters. PSI:PI Ion a-NH3 parameter information, type of product: a ion with lost ammonia. MS MS:1001146 param: a ion-NH3 DEPRECATED Ion a-NH3 parameter information, type of product: a ion with lost ammonia. PSI:PI MS MS:1001147 protein ambiguity group result details Ion a-H2O if a significant and fragment includes STED. MS MS:1001148 param: a ion-H2O DEPRECATED Ion a-H2O if a significant and fragment includes STED. PSI:PI Ion b-NH3 parameter information, type of product: b ion with lost ammonia. MS MS:1001149 param: b ion-NH3 DEPRECATED Ion b-NH3 parameter information, type of product: b ion with lost ammonia. PSI:PI Ion b-H2O if b significant and fragment includes STED. MS MS:1001150 param: b ion-H2O DEPRECATED Ion b-H2O if b significant and fragment includes STED. PSI:PI Ion y-NH3 parameter information, type of product: y ion with lost ammonia. MS MS:1001151 param: y ion-NH3 DEPRECATED Ion y-NH3 parameter information, type of product: y ion with lost ammonia. PSI:PI MS MS:1001152 This term was made obsolete - use MS:1001262 and MS:1002455 instead. param: y ion-H2O DEPRECATED Search engine specific scores. MS MS:1001153 search engine specific score Search engine specific scores. PSI:PI The SEQUEST result 'Probability'. MS MS:1001154 SEQUEST:probability The SEQUEST result 'Probability'. PSI:PI The SEQUEST result 'XCorr'. MS MS:1001155 SEQUEST:xcorr The SEQUEST result 'XCorr'. PSI:PI The SEQUEST result 'DeltaCn'. MS MS:1001156 SEQUEST:deltacn The SEQUEST result 'DeltaCn'. PSI:PI The SEQUEST result 'Sp' (protein). MS MS:1001157 SEQUEST:sp The SEQUEST result 'Sp' (protein). PSI:PI MS MS:1001158 SEQUEST:Uniq The SEQUEST result 'Expectation value'. MS MS:1001159 SEQUEST:expectation value The SEQUEST result 'Expectation value'. PSI:PI The SEQUEST result 'Sf'. MS MS:1001160 SEQUEST:sf The SEQUEST result 'Sf'. PSI:PI The SEQUEST result 'Matched Ions'. MS MS:1001161 SEQUEST:matched ions The SEQUEST result 'Matched Ions'. PSI:PI The SEQUEST result 'Total Ions'. MS MS:1001162 SEQUEST:total ions The SEQUEST result 'Total Ions'. PSI:PI The SEQUEST result 'Consensus Score'. MS MS:1001163 SEQUEST:consensus score The SEQUEST result 'Consensus Score'. PSI:PI The Paragon result 'Unused ProtScore'. MS MS:1001164 Paragon:unused protscore The Paragon result 'Unused ProtScore'. PSI:PI The Paragon result 'Total ProtScore'. MS MS:1001165 Paragon:total protscore The Paragon result 'Total ProtScore'. PSI:PI The Paragon result 'Score'. MS MS:1001166 Paragon:score The Paragon result 'Score'. PSI:PI The Paragon result 'Confidence'. MS MS:1001167 Paragon:confidence The Paragon result 'Confidence'. PSI:PI The Paragon result 'Expression Error Factor'. MS MS:1001168 Paragon:expression error factor The Paragon result 'Expression Error Factor'. PSI:PI The Paragon result 'Expression change P-value'. MS MS:1001169 Paragon:expression change p-value The Paragon result 'Expression change P-value'. PSI:PI The Paragon result 'Contrib'. MS MS:1001170 Paragon:contrib The Paragon result 'Contrib'. PSI:PI The Mascot result 'Score'. MS MS:1001171 Mascot:score The Mascot result 'Score'. PSI:PI The Mascot result 'expectation value'. MS MS:1001172 Mascot:expectation value The Mascot result 'expectation value'. PSI:PI The Mascot result 'Matched ions'. MS MS:1001173 Mascot:matched ions The Mascot result 'Matched ions'. PSI:PI The Mascot result 'Total ions'. MS MS:1001174 Mascot:total ions The Mascot result 'Total ions'. PSI:PI A peptide matching multiple proteins. MS MS:1001175 peptide shared in multiple proteins A peptide matching multiple proteins. PSI:PI Regular expression for Trypsin. MS MS:1001176 (?<=[KR])(?!P) Regular expression for Trypsin. PSI:PI Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search. MS MS:1001177 number of molecular hypothesis considered Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search. PSI:PI Expressed sequence tag nucleotide sequence database. MS MS:1001178 database EST Expressed sequence tag nucleotide sequence database. PSI:PI Regular expressions for cleavage enzymes. MS MS:1001180 Cleavage agent regular expression Regular expressions for cleavage enzymes. PSI:PI The details of the actual run of the search. MS MS:1001184 search statistics The details of the actual run of the search. PSI:PI Mobilion MBI file format. MS MS:1001185 Mobilion MBI format Mobilion MBI file format. PSI:MS Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. MS MS:1001186 Mobilion MBI nativeID format Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. PSI:MS As parameter for search engine: apply the modification only at the N-terminus of a peptide. MS MS:1001189 modification specificity peptide N-term As parameter for search engine: apply the modification only at the N-terminus of a peptide. PSI:PI As parameter for search engine: apply the modification only at the C-terminus of a peptide. MS MS:1001190 modification specificity peptide C-term As parameter for search engine: apply the modification only at the C-terminus of a peptide. PSI:PI OBSOLETE Quality estimation by p-value. MS MS:1001191 This term was made obsolete because now is split into peptide and protein terms. p-value true OBSOLETE Quality estimation by p-value. PSI:PI Result of quality estimation: Expect value. MS MS:1001192 Expect value Result of quality estimation: Expect value. PSI:PI Result of quality estimation: confidence score. MS MS:1001193 confidence score Result of quality estimation: confidence score. PSI:PI Quality estimation by decoy database. MS MS:1001194 quality estimation with decoy database Quality estimation by decoy database. PSI:PI Decoy type: Amino acids of protein sequences are used in reverse order. MS MS:1001195 decoy DB type reverse Decoy type: Amino acids of protein sequences are used in reverse order. PSI:PI Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass). MS MS:1001196 decoy DB type randomized Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass). PSI:PI Decoy database composition: database contains original (target) and decoy entries. MS MS:1001197 DB composition target+decoy Decoy database composition: database contains original (target) and decoy entries. PSI:PI Identification confidence metric for a protein. MS MS:1001198 protein identification confidence metric Identification confidence metric for a protein. PSI:PI Source file for this mzIdentML was in Mascot DAT file format. MS MS:1001199 Mascot DAT format Source file for this mzIdentML was in Mascot DAT file format. PSI:PI Source file for this mzIdentML was in SEQUEST out file format. MS MS:1001200 SEQUEST out file format Source file for this mzIdentML was in SEQUEST out file format. PSI:PI Maximum value of molecular weight filter. MS MS:1001201 DB MW filter maximum Maximum value of molecular weight filter. PSI:PI Minimum value of molecular weight filter. MS MS:1001202 DB MW filter minimum Minimum value of molecular weight filter. PSI:PI Maximum value of isoelectric point filter. MS MS:1001203 DB PI filter maximum Maximum value of isoelectric point filter. PSI:PI Minimum value of isoelectric point filter. MS MS:1001204 DB PI filter minimum Minimum value of isoelectric point filter. PSI:PI The name of the Mascot search engine. MS MS:1001207 Mascot The name of the Mascot search engine. PSI:PI The name of the SEQUEST search engine. MS MS:1001208 SEQUEST The name of the SEQUEST search engine. PSI:PI The name of the Phenyx search engine. MS MS:1001209 Phenyx The name of the Phenyx search engine. PSI:PI The type of mass difference value to be considered by the search engine (monoisotopic or average). MS MS:1001210 mass type settings The type of mass difference value to be considered by the search engine (monoisotopic or average). PSI:PI Mass type setting for parent mass was monoisotopic. MS MS:1001211 parent mass type mono Mass type setting for parent mass was monoisotopic. PSI:PI Mass type setting for parent mass was average isotopic. MS MS:1001212 parent mass type average Mass type setting for parent mass was average isotopic. PSI:PI OBSOLETE: Scores and global result characteristics. MS MS:1001213 This former purgatory term was made obsolete. search result details true OBSOLETE: Scores and global result characteristics. PSI:PI Estimation of the global false discovery rate of proteins. MS MS:1001214 protein-level global FDR Estimation of the global false discovery rate of proteins. PSI:PI The SEQUEST result 'Sp' in out file (peptide). MS MS:1001215 SEQUEST:PeptideSp The SEQUEST result 'Sp' in out file (peptide). PSI:PI The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'. MS MS:1001217 SEQUEST:PeptideRankSp The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'. PSI:PI The SEQUEST result '#' in out file (peptide). MS MS:1001218 SEQUEST:PeptideNumber The SEQUEST result '#' in out file (peptide). PSI:PI The SEQUEST result 'Id#' in out file (peptide). MS MS:1001219 SEQUEST:PeptideIdnumber The SEQUEST result 'Id#' in out file (peptide). PSI:PI Fragmentation information, type of product: y ion. MS MS:1001220 frag: y ion Fragmentation information, type of product: y ion. PSI:PI Fragmentation information like ion types. MS MS:1001221 product ion attribute Fragmentation information like ion types. PSI:PI Fragmentation information, type of product: b ion without water. MS MS:1001222 frag: b ion - H2O Fragmentation information, type of product: b ion without water. PSI:PI Fragmentation information, type of product: y ion without water. MS MS:1001223 frag: y ion - H2O Fragmentation information, type of product: y ion without water. PSI:PI Fragmentation information, type of product: b ion. MS MS:1001224 frag: b ion Fragmentation information, type of product: b ion. PSI:PI The m/z of the product ion. fragment ion m/z MS MS:1001225 product ion m/z The m/z of the product ion. PSI:PI The intensity of a single product ion. fragment ion intensity MS MS:1001226 product ion intensity The intensity of a single product ion. PSI:PI The product ion m/z error. MS MS:1001227 product ion m/z error The product ion m/z error. PSI:PI Fragmentation information, type of product: x ion. MS MS:1001228 frag: x ion Fragmentation information, type of product: x ion. PSI:PI Fragmentation information, type of product: a ion. MS MS:1001229 frag: a ion Fragmentation information, type of product: a ion. PSI:PI Fragmentation information, type of product: z ion. MS MS:1001230 frag: z ion Fragmentation information, type of product: z ion. PSI:PI Fragmentation information, type of product: c ion. MS MS:1001231 frag: c ion Fragmentation information, type of product: c ion. PSI:PI Ion b-NH3 fragmentation information, type of product: b ion without ammonia. MS MS:1001232 frag: b ion - NH3 Ion b-NH3 fragmentation information, type of product: b ion without ammonia. PSI:PI Ion y-NH3 fragmentation information, type of product: y ion without ammonia. MS MS:1001233 frag: y ion - NH3 Ion y-NH3 fragmentation information, type of product: y ion without ammonia. PSI:PI Fragmentation information, type of product: a ion without water. MS MS:1001234 frag: a ion - H2O Fragmentation information, type of product: a ion without water. PSI:PI Ion a-NH3 fragmentation information, type of product: a ion without ammonia. MS MS:1001235 frag: a ion - NH3 Ion a-NH3 fragmentation information, type of product: a ion without ammonia. PSI:PI Fragmentation information, type of product: d ion. MS MS:1001236 frag: d ion Fragmentation information, type of product: d ion. PSI:PI Fragmentation information, type of product: v ion. MS MS:1001237 frag: v ion Fragmentation information, type of product: v ion. PSI:PI Fragmentation information, type of product: w ion. MS MS:1001238 frag: w ion Fragmentation information, type of product: w ion. PSI:PI Fragmentation information, type of product: immonium ion. MS MS:1001239 frag: immonium ion Fragmentation information, type of product: immonium ion. PSI:PI Non-identified ion. MS MS:1001240 non-identified ion Non-identified ion. PSI:PI Co-eluting ion. MS MS:1001241 co-eluting ion Co-eluting ion. PSI:PI Source file for this mzIdentML was a SEQUEST folder with its out files. MS MS:1001242 SEQUEST out folder Source file for this mzIdentML was a SEQUEST folder with its out files. PSI:PI Source file for this mzIdentML was a SEQUEST summary page (proteins). MS MS:1001243 SEQUEST summary Source file for this mzIdentML was a SEQUEST summary page (proteins). PSI:PI PerSeptive peak list file format. MS MS:1001245 PerSeptive PKS format PerSeptive peak list file format. http://www.matrixscience.com/help/data_file_help.html#PKS PE SCIEX peak list file format. MS MS:1001246 SCIEX API III format PE SCIEX peak list file format. http://www.matrixscience.com/help/data_file_help.html#API Bruker data exchange XML format. MS MS:1001247 Bruker XML format Bruker data exchange XML format. PSI:PI Details describing the search input. MS MS:1001249 search input details Details describing the search input. PSI:PI Result of quality estimation: the local FDR at the current position of a sorted list. MS MS:1001250 local FDR Result of quality estimation: the local FDR at the current position of a sorted list. PSI:PI Enzyme trypsin. MS MS:1001251 Trypsin Enzyme trypsin. PSI:PI Database source EBI. MS MS:1001252 DB source EBI Database source EBI. PSI:PI Database source NCBI. MS MS:1001253 DB source NCBI Database source NCBI. PSI:PI Database source UniProt. MS MS:1001254 DB source UniProt Database source UniProt. PSI:PI Mass type setting for fragment mass was average isotopic. MS MS:1001255 fragment mass type average Mass type setting for fragment mass was average isotopic. PSI:PI Mass type setting for fragment mass was monoisotopic. MS MS:1001256 fragment mass type mono Mass type setting for fragment mass was monoisotopic. PSI:PI Parameter information, type of product: side chain loss v ion. MS MS:1001257 param: v ion Parameter information, type of product: side chain loss v ion. PSI:PI Parameter information, type of product: side chain loss d ion. MS MS:1001258 param: d ion Parameter information, type of product: side chain loss d ion. PSI:PI Parameter information, type of product: immonium ion. MS MS:1001259 param: immonium ion Parameter information, type of product: immonium ion. PSI:PI Parameter information, type of product: side chain loss w ion. MS MS:1001260 param: w ion Parameter information, type of product: side chain loss w ion. PSI:PI Parameter information, type of product: x ion with charge on the C-terminal side. MS MS:1001261 param: x ion Parameter information, type of product: x ion with charge on the C-terminal side. PSI:PI Parameter information, type of product: y ion with charge on the C-terminal side. MS MS:1001262 param: y ion Parameter information, type of product: y ion with charge on the C-terminal side. PSI:PI Parameter information, type of product: z ion with charge on the C-terminal side. MS MS:1001263 param: z ion Parameter information, type of product: z ion with charge on the C-terminal side. PSI:PI Role of a Person or Organization. MS MS:1001266 role type Role of a Person or Organization. PSI:PI Software vendor role. MS MS:1001267 software vendor Software vendor role. PSI:PI Programmer role. MS MS:1001268 programmer Programmer role. PSI:PI Instrument vendor role. MS MS:1001269 instrument vendor Instrument vendor role. PSI:PI Lab personnel role. MS MS:1001270 lab personnel Lab personnel role. PSI:PI Researcher role. MS MS:1001271 researcher Researcher role. PSI:PI Regular expression for Arg-C. MS MS:1001272 (?<=R)(?!P) Regular expression for Arg-C. PSI:PI Regular expression for Asp-N. MS MS:1001273 (?=[BD]) Regular expression for Asp-N. PSI:PI Regular expression for Asp-N-ambic. MS MS:1001274 (?=[DE]) Regular expression for Asp-N-ambic. PSI:PI Source data for this mzIdentML was a ProteinScape SearchEvent. MS MS:1001275 ProteinScape SearchEvent Source data for this mzIdentML was a ProteinScape SearchEvent. PSI:PI Source data for this mzIdentML was a ProteinScape Gel. MS MS:1001276 ProteinScape Gel Source data for this mzIdentML was a ProteinScape Gel. PSI:PI Specify the regular expression for decoy accession numbers. MS MS:1001283 decoy DB accession regexp Specify the regular expression for decoy accession numbers. PSI:PI OBSOLETE The name of the database, the search database was derived from. MS MS:1001284 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB derived from true OBSOLETE The name of the database, the search database was derived from. PSI:PI International Protein Index database for Mus musculus sequences. MS MS:1001285 database IPI_mouse International Protein Index database for Mus musculus sequences. PSI:PI International Protein Index database for Rattus norvegicus sequences. MS MS:1001286 database IPI_rat International Protein Index database for Rattus norvegicus sequences. PSI:PI International Protein Index database for Danio rerio sequences. MS MS:1001287 database IPI_zebrafish International Protein Index database for Danio rerio sequences. PSI:PI International Protein Index database for Gallus gallus sequences. MS MS:1001288 database IPI_chicken International Protein Index database for Gallus gallus sequences. PSI:PI International Protein Index database for Bos taurus sequences. MS MS:1001289 database IPI_cow International Protein Index database for Bos taurus sequences. PSI:PI International Protein Index database for Arabidopsis thaliana sequences. MS MS:1001290 database IPI_arabidopsis International Protein Index database for Arabidopsis thaliana sequences. PSI:PI OBSOLETE Decoy database from a non-redundant GenBank sequence database. MS MS:1001291 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from nr true OBSOLETE Decoy database from a non-redundant GenBank sequence database. PSI:PI OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus. MS MS:1001292 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from IPI_rat true OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus. PSI:PI OBSOLETE Decoy database from a International Protein Index database for Mus musculus. MS MS:1001293 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from IPI_mouse true OBSOLETE Decoy database from a International Protein Index database for Mus musculus. PSI:PI OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana. MS MS:1001294 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from IPI_arabidopsis true OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana. PSI:PI OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database. MS MS:1001295 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from EST true OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database. PSI:PI OBSOLETE Decoy database from a International Protein Index database for Danio rerio. MS MS:1001296 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from IPI_zebrafish true OBSOLETE Decoy database from a International Protein Index database for Danio rerio. PSI:PI OBSOLETE Decoy database from a Swiss-Prot protein sequence database. MS MS:1001297 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from UniProtKB/Swiss-Prot true OBSOLETE Decoy database from a Swiss-Prot protein sequence database. PSI:PI OBSOLETE Decoy database from a International Protein Index database for Gallus gallus. MS MS:1001298 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from IPI_chicken true OBSOLETE Decoy database from a International Protein Index database for Gallus gallus. PSI:PI OBSOLETE Decoy database from a International Protein Index database for Bos taurus. MS MS:1001299 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from IPI_cow true OBSOLETE Decoy database from a International Protein Index database for Bos taurus. PSI:PI OBSOLETE Decoy database from a International Protein Index database for Homo sapiens. MS MS:1001300 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from IPI_human true OBSOLETE Decoy database from a International Protein Index database for Homo sapiens. PSI:PI The rank of the protein in a list sorted by the search engine. MS MS:1001301 protein rank The rank of the protein in a list sorted by the search engine. PSI:PI Search engine specific input parameters. MS MS:1001302 search engine specific input parameter Search engine specific input parameters. PSI:PI Endoproteinase Arg-C. Clostripain Trypsin/R MS MS:1001303 Arg-C Endoproteinase Arg-C. PSI:PI Endoproteinase Asp-N. MS MS:1001304 Asp-N Endoproteinase Asp-N. PSI:PI Enzyme Asp-N, Ammonium Bicarbonate (AmBic). MS MS:1001305 Asp-N_ambic Enzyme Asp-N, Ammonium Bicarbonate (AmBic). PSI:PI Enzyme chymotrypsin. MS MS:1001306 Chymotrypsin Enzyme chymotrypsin. PSI:PI Cyanogen bromide. MS MS:1001307 CNBr Cyanogen bromide. PSI:PI Formic acid. MS MS:1001308 Formic_acid Formic acid. PubChem_Compound:284 Endoproteinase Lys-C. Trypsin/K MS MS:1001309 Lys-C Endoproteinase Lys-C. PSI:PI Proteinase Lys-C/P. MS MS:1001310 Lys-C/P Proteinase Lys-C/P. PSI:PI PepsinA proteinase. MS MS:1001311 PepsinA PepsinA proteinase. PSI:PI Cleavage agent TrypChymo. MS MS:1001312 TrypChymo Cleavage agent TrypChymo. PSI:PI Cleavage agent Trypsin/P. MS MS:1001313 Trypsin/P Cleavage agent Trypsin/P. PSI:PI Cleavage agent V8-DE. MS MS:1001314 V8-DE Cleavage agent V8-DE. PSI:PI Cleavage agent V8-E. MS MS:1001315 V8-E Cleavage agent V8-E. PSI:PI Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05). MS MS:1001316 Mascot:SigThreshold Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05). PSI:PI The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1. MS MS:1001317 Mascot:MaxProteinHits The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1. PSI:PI Mascot protein scoring method; either 'Standard' or 'MudPIT'. MS MS:1001318 Mascot:ProteinScoringMethod Mascot protein scoring method; either 'Standard' or 'MudPIT'. PSI:PI Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed. MS MS:1001319 Mascot:MinMSMSThreshold Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed. PSI:PI If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed. MS MS:1001320 Mascot:ShowHomologousProteinsWithSamePeptides If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed. PSI:PI If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed. MS MS:1001321 Mascot:ShowHomologousProteinsWithSubsetOfPeptides If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed. PSI:PI Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits. MS MS:1001322 Mascot:RequireBoldRed Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits. PSI:PI If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use. MS MS:1001323 Mascot:UseUnigeneClustering If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use. PSI:PI If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included. MS MS:1001324 Mascot:IncludeErrorTolerantMatches If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included. http://www.matrixscience.com/help/error_tolerant_help.html If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database. MS MS:1001325 Mascot:ShowDecoyMatches If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database. PSI:PI OBSOLETE. MS MS:1001326 This former purgatory term was made obsolete. add_others true OBSOLETE. PSI:PI Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data. MS MS:1001327 Spectronaut Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data. https://doi.org/10.1074/mcp.M114.044305 OMSSA E-value. MS MS:1001328 OMSSA:evalue OMSSA E-value. PSI:PI OMSSA p-value. MS MS:1001329 OMSSA:pvalue OMSSA p-value. PSI:PI The X!Tandem expectation value. MS MS:1001330 X!Tandem:expect The X!Tandem expectation value. PSI:PI The X!Tandem hyperscore. MS MS:1001331 X!Tandem:hyperscore The X!Tandem hyperscore. PSI:PI Regular expression for Chymotrypsin. MS MS:1001332 (?<=[FYWL])(?!P) Regular expression for Chymotrypsin. PSI:PI Regular expression for CNBr. MS MS:1001333 (?<=M) Regular expression for CNBr. PSI:PI Regular expression for formic acid. MS MS:1001334 ((?<=D))|((?=D)) Regular expression for formic acid. PSI:PI Regular expression for Lys-C. MS MS:1001335 (?<=K)(?!P) Regular expression for Lys-C. PSI:PI Regular expression for Lys-C/P. MS MS:1001336 (?<=K) Regular expression for Lys-C/P. PSI:PI Regular expression for PepsinA. MS MS:1001337 (?<=[FL]) Regular expression for PepsinA. PSI:PI Regular expression for TrypChymo. MS MS:1001338 (?<=[FYWLKR])(?!P) Regular expression for TrypChymo. PSI:PI Regular expression for Trypsin/P. MS MS:1001339 (?<=[KR]) Regular expression for Trypsin/P. PSI:PI Regular expression for V8-DE. MS MS:1001340 (?<=[BDEZ])(?!P) Regular expression for V8-DE. PSI:PI Regular expression for V8-E. MS MS:1001341 (?<=[EZ])(?!P) Regular expression for V8-E. PSI:PI Details about a single database sequence. MS MS:1001342 database sequence details Details about a single database sequence. PSI:PI The sequence is a nucleic acid sequence. MS MS:1001343 NA sequence The sequence is a nucleic acid sequence. PSI:PI The sequence is a amino acid sequence. MS MS:1001344 AA sequence The sequence is a amino acid sequence. PSI:PI Children of this term specify the source of the mass table used. MS MS:1001345 mass table source Children of this term specify the source of the mass table used. PSI:PI The masses used in the mass table are taken from AAIndex. MS MS:1001346 AAIndex mass table The masses used in the mass table are taken from AAIndex. PSI:PI The children of this term define file formats of the sequence database used. MS MS:1001347 database file formats The children of this term define file formats of the sequence database used. PSI:PI The sequence database was stored in the FASTA format. MS MS:1001348 FASTA format The sequence database was stored in the FASTA format. PSI:PI The sequence database was stored in the Abstract Syntax Notation 1 format. MS MS:1001349 ASN.1 The sequence database was stored in the Abstract Syntax Notation 1 format. PSI:PI The sequence database was stored in the NCBI formatdb (*.p*) format. MS MS:1001350 NCBI *.p* The sequence database was stored in the NCBI formatdb (*.p*) format. PSI:PI ClustalW ALN (multiple alignment) format. MS MS:1001351 clustal aln ClustalW ALN (multiple alignment) format. PSI:PI EMBL entry format. MS MS:1001352 embl em EMBL entry format. PSI:PI The NBRF PIR was used as format. MS MS:1001353 NBRF PIR The NBRF PIR was used as format. PSI:PI Root node for options for the mass table used. MS MS:1001354 mass table options Root node for options for the mass table used. PSI:PI Descriptions of peptides. MS MS:1001355 peptide descriptions Descriptions of peptides. PSI:PI Descriptions of the input spectra. MS MS:1001356 spectrum descriptions Descriptions of the input spectra. PSI:PI Description of the quality of the input spectrum. MS MS:1001357 spectrum quality descriptions Description of the quality of the input spectrum. PSI:PI This term reports the quality of the spectrum assigned by msmsEval. MS MS:1001358 msmsEval quality This term reports the quality of the spectrum assigned by msmsEval. PSI:PI Children of this term describe ambiguous residues. MS MS:1001359 ambiguous residues Children of this term describe ambiguous residues. PSI:PI List of standard residue one letter codes which are used to replace a non-standard. MS MS:1001360 alternate single letter codes List of standard residue one letter codes which are used to replace a non-standard. PSI:PI List of masses a non-standard letter code is replaced with. MS MS:1001361 alternate mass List of masses a non-standard letter code is replaced with. PSI:PI The number of unmatched peaks. MS MS:1001362 number of unmatched peaks The number of unmatched peaks. PSI:PI A peptide matching only one. MS MS:1001363 peptide unique to one protein A peptide matching only one. PSI:PI Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). MS MS:1001364 peptide sequence-level global FDR Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). PSI:PI Fragmentation information, type of product: internal yb ion. MS MS:1001365 frag: internal yb ion Fragmentation information, type of product: internal yb ion. PSI:PI Fragmentation information, type of product: internal ya ion. MS MS:1001366 frag: internal ya ion Fragmentation information, type of product: internal ya ion. PSI:PI Fragmentation information, type of product: z+1 ion. MS MS:1001367 frag: z+1 ion Fragmentation information, type of product: z+1 ion. PSI:PI Fragmentation information, type of product: z+2 ion. MS MS:1001368 frag: z+2 ion Fragmentation information, type of product: z+2 ion. PSI:PI Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search. MS MS:1001369 text format Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search. PSI:PI The Mascot result 'homology threshold'. MS MS:1001370 Mascot:homology threshold The Mascot result 'homology threshold'. PSI:PI The Mascot result 'identity threshold'. MS MS:1001371 Mascot:identity threshold The Mascot result 'identity threshold'. PSI:PI MS MS:1001372 SEQUEST:Sequences SEQUEST total ion current. MS MS:1001373 SEQUEST:TIC SEQUEST total ion current. PSI:PI MS MS:1001374 SEQUEST:Sum The instrument type parameter value in Phenyx. MS MS:1001375 Phenyx:Instrument Type The instrument type parameter value in Phenyx. PSI:PI The selected scoring model in Phenyx. MS MS:1001376 Phenyx:Scoring Model The selected scoring model in Phenyx. PSI:PI The default parent charge value in Phenyx. MS MS:1001377 Phenyx:Default Parent Charge The default parent charge value in Phenyx. PSI:PI The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct. MS MS:1001378 Phenyx:Trust Parent Charge The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct. PSI:PI The turbo mode parameter in Phenyx. MS MS:1001379 Phenyx:Turbo The turbo mode parameter in Phenyx. PSI:PI The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx. MS MS:1001380 Phenyx:Turbo:ErrorTol The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx. PSI:PI The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx. MS MS:1001381 Phenyx:Turbo:Coverage The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx. PSI:PI The list of ion series considered in the turbo mode of Phenyx. MS MS:1001382 Phenyx:Turbo:Series The list of ion series considered in the turbo mode of Phenyx. PSI:PI The minimal number of residues for a peptide to be considered for a valid identification in Phenyx. MS MS:1001383 Phenyx:MinPepLength The minimal number of residues for a peptide to be considered for a valid identification in Phenyx. PSI:PI The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx. MS MS:1001384 Phenyx:MinPepzscore The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx. PSI:PI The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx. MS MS:1001385 Phenyx:MaxPepPvalue The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx. PSI:PI The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx. MS MS:1001386 Phenyx:AC Score The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx. PSI:PI The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used. MS MS:1001387 Phenyx:Conflict Resolution The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used. PSI:PI The primary sequence database identifier of a protein in Phenyx. MS MS:1001388 Phenyx:AC The primary sequence database identifier of a protein in Phenyx. PSI:PI A secondary sequence database identifier of a protein in Phenyx. MS MS:1001389 Phenyx:ID A secondary sequence database identifier of a protein in Phenyx. PSI:PI The protein score of a protein match in Phenyx. MS MS:1001390 Phenyx:Score The protein score of a protein match in Phenyx. PSI:PI First number of phenyx result "#Peptides". MS MS:1001391 Phenyx:Peptides1 First number of phenyx result "#Peptides". PSI:PI Second number of phenyx result "#Peptides". MS MS:1001392 Phenyx:Peptides2 Second number of phenyx result "#Peptides". PSI:PI The value of the automatic peptide acceptance filter in Phenyx. MS MS:1001393 Phenyx:Auto The value of the automatic peptide acceptance filter in Phenyx. PSI:PI The value of the user-defined peptide acceptance filter in Phenyx. MS MS:1001394 Phenyx:User The value of the user-defined peptide acceptance filter in Phenyx. PSI:PI The z-score value of a peptide sequence match in Phenyx. MS MS:1001395 Phenyx:Pepzscore The z-score value of a peptide sequence match in Phenyx. PSI:PI The p-value of a peptide sequence match in Phenyx. MS MS:1001396 Phenyx:PepPvalue The p-value of a peptide sequence match in Phenyx. PSI:PI The number of missed cleavages of a peptide sequence in Phenyx. MS MS:1001397 Phenyx:NumberOfMC The number of missed cleavages of a peptide sequence in Phenyx. PSI:PI The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx. MS MS:1001398 Phenyx:Modif The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx. PSI:PI Source file for this mzIdentML was in OMSSA csv file format. MS MS:1001399 OMSSA csv format Source file for this mzIdentML was in OMSSA csv file format. PSI:PI Source file for this mzIdentML was in OMSSA xml file format. MS MS:1001400 OMSSA xml format Source file for this mzIdentML was in OMSSA xml file format. PSI:PI Source file for this mzIdentML was in X!Tandem xml file format. MS MS:1001401 X!Tandem xml format Source file for this mzIdentML was in X!Tandem xml file format. PSI:PI This subsection describes terms which can describe details of spectrum identification results. MS MS:1001405 spectrum identification result details This subsection describes terms which can describe details of spectrum identification results. PSI:PI Parameter information, type of product: internal yb ion. MS MS:1001406 param: internal yb ion Parameter information, type of product: internal yb ion. PSI:PI Parameter information, type of product: internal ya ion. MS MS:1001407 param: internal ya ion Parameter information, type of product: internal ya ion. PSI:PI Parameter information, type of product: z+1 ion. MS MS:1001408 param: z+1 ion Parameter information, type of product: z+1 ion. PSI:PI Parameter information, type of product: z+2 ion. MS MS:1001409 param: z+2 ion Parameter information, type of product: z+2 ion. PSI:PI The translation start codons used to translate the nucleotides to amino acids. MS MS:1001410 translation start codons The translation start codons used to translate the nucleotides to amino acids. PSI:PI Specification of the search tolerance. MS MS:1001411 search tolerance specification Specification of the search tolerance. PSI:PI MS MS:1001412 search tolerance plus value MS MS:1001413 search tolerance minus value OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file. MS:1000797 MS MS:1001414 MGF scans true OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file. PSI:PI OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file. MS:1000798 MS MS:1001415 MGF raw scans true OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file. PSI:PI OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE. MS:1000796 MS MS:1001416 spectrum title true OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE. PSI:PI SpectraST dot product of two spectra, measuring spectral similarity. MS MS:1001417 SpectraST:dot SpectraST dot product of two spectra, measuring spectral similarity. PSI:PI SpectraST measure of how much of the dot product is dominated by a few peaks. MS MS:1001418 SpectraST:dot_bias SpectraST measure of how much of the dot product is dominated by a few peaks. PSI:PI SpectraST spectrum score. MS MS:1001419 SpectraST:discriminant score F SpectraST spectrum score. PSI:PI SpectraST normalised difference between dot product of top hit and runner-up. MS MS:1001420 SpectraST:delta SpectraST normalised difference between dot product of top hit and runner-up. PSI:PI The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers. MS MS:1001421 pepXML format The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers. PSI:PI The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers. MS MS:1001422 protXML format The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers. PSI:PI A URL that describes the translation table used to translate the nucleotides to amino acids. MS MS:1001423 translation table description A URL that describes the translation table used to translate the nucleotides to amino acids. PSI:PI Name of the used method in the ProteinExtractor algorithm. MS MS:1001424 ProteinExtractor:Methodname Name of the used method in the ProteinExtractor algorithm. PSI:PI Flag indicating if a non redundant scoring should be generated. MS MS:1001425 ProteinExtractor:GenerateNonRedundant Flag indicating if a non redundant scoring should be generated. PSI:PI Flag indicating if identified proteins should be included. MS MS:1001426 ProteinExtractor:IncludeIdentified Flag indicating if identified proteins should be included. PSI:PI The maximum number of proteins to consider. MS MS:1001427 ProteinExtractor:MaxNumberOfProteins The maximum number of proteins to consider. PSI:PI The maximum considered mass for a protein. MS MS:1001428 ProteinExtractor:MaxProteinMass The maximum considered mass for a protein. PSI:PI The minimum number of proteins to consider. MS MS:1001429 ProteinExtractor:MinNumberOfPeptides The minimum number of proteins to consider. PSI:PI Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score. MS MS:1001430 ProteinExtractor:UseMascot Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score. PSI:PI Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score. MS MS:1001431 ProteinExtractor:MascotPeptideScoreThreshold Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score. DOI:10.4172/jpb.1000056 In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation. MS MS:1001432 ProteinExtractor:MascotUniqueScore In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation. DOI:10.4172/jpb.1000056 MS MS:1001433 ProteinExtractor:MascotUseIdentityScore Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. MS MS:1001434 ProteinExtractor:MascotWeighting Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. DOI:10.4172/jpb.1000056 Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score. MS MS:1001435 ProteinExtractor:UseSequest Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score. PSI:PI Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score. MS MS:1001436 ProteinExtractor:SequestPeptideScoreThreshold Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score. DOI:10.4172/jpb.1000056 In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation. MS MS:1001437 ProteinExtractor:SequestUniqueScore In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation. DOI:10.4172/jpb.1000056 Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. MS MS:1001438 ProteinExtractor:SequestWeighting Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. DOI:10.4172/jpb.1000056 Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score. MS MS:1001439 ProteinExtractor:UseProteinSolver Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score. PSI:PI Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score. MS MS:1001440 ProteinExtractor:ProteinSolverPeptideScoreThreshold Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score. DOI:10.4172/jpb.1000056 In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation. MS MS:1001441 ProteinExtractor:ProteinSolverUniqueScore In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation. DOI:10.4172/jpb.1000056 Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. MS MS:1001442 ProteinExtractor:ProteinSolverWeighting Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. DOI:10.4172/jpb.1000056 Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score. MS MS:1001443 ProteinExtractor:UsePhenyx Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score. PSI:PI Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score. MS MS:1001444 ProteinExtractor:PhenyxPeptideScoreThreshold Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score. DOI:10.4172/jpb.1000056 In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation. MS MS:1001445 ProteinExtractor:PhenyxUniqueScore In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation. DOI:10.4172/jpb.1000056 Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. MS MS:1001446 ProteinExtractor:PhenyxWeighting Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. DOI:10.4172/jpb.1000056 False-discovery rate threshold for proteins. MS MS:1001447 prot:FDR threshold False-discovery rate threshold for proteins. PSI:PI False-discovery rate threshold for peptides. MS MS:1001448 pep:FDR threshold False-discovery rate threshold for peptides. PSI:PI Threshold for OMSSA e-value for quality estimation. MS MS:1001449 OMSSA e-value threshold Threshold for OMSSA e-value for quality estimation. PSI:PI Details of decoy generation and database structure. MS MS:1001450 decoy DB details Details of decoy generation and database structure. PSI:PI Name of algorithm used for decoy generation. MS MS:1001451 decoy DB generation algorithm Name of algorithm used for decoy generation. PSI:PI Decoy type: Amino acids of protein sequences are used in a random order. MS MS:1001452 decoy DB type shuffle Decoy type: Amino acids of protein sequences are used in a random order. PSI:PI Decoy database composition: database contains only decoy entries. MS MS:1001453 DB composition only decoy Decoy database composition: database contains only decoy entries. PSI:PI Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy). MS MS:1001454 quality estimation with implicite decoy sequences Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy). PSI:PI Acquisition software. MS MS:1001455 acquisition software Acquisition software. PSI:MS Analysis software. MS MS:1001456 analysis software Analysis software. PSI:MS Data processing software. MS MS:1001457 data processing software Data processing software. PSI:MS Vocabularies describing the spectrum generation information. MS MS:1001458 spectrum generation information Vocabularies describing the spectrum generation information. PSI:PI Format of data files. MS MS:1001459 file format Format of data files. PSI:MS This term should be given if the modification was unknown. MS MS:1001460 unknown modification This term should be given if the modification was unknown. PSI:PI Greylag identification software. MS MS:1001461 greylag Greylag identification software. http://greylag.org/ The sequence database was stored in the PEFF (PSI enhanced FastA file) format. MS MS:1001462 PEFF format The sequence database was stored in the PEFF (PSI enhanced FastA file) format. PSI:PI Phenyx open XML file format. MS MS:1001463 Phenyx XML format Phenyx open XML file format. PSI:PI DTASelect file format. MS MS:1001464 DTASelect format DTASelect file format. PMID:12643522 http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html MS2 file format for MS2 spectral data. MS MS:1001466 MS2 format MS2 file format for MS2 spectral data. DOI:10.1002/rcm.1603 PMID:15317041 http://fields.scripps.edu/sequest/SQTFormat.html This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens. MS MS:1001467 taxonomy: NCBI TaxID This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens. PSI:PI This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. MS MS:1001468 taxonomy: common name This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. PSI:PI This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. MS MS:1001469 taxonomy: scientific name This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. PSI:PI This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. MS MS:1001470 taxonomy: Swiss-Prot ID This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. PSI:PI The children of this term can be used to describe modifications. MS MS:1001471 peptide modification details The children of this term can be used to describe modifications. PSI:PI Representation of an array of the measurements of a selectively monitored ion versus time. SIM chromatogram MS MS:1001472 selected ion monitoring chromatogram Representation of an array of the measurements of a selectively monitored ion versus time. PSI:MS Representation of an array of the measurements of a selectively monitored reaction versus time. SRM chromatogram MS MS:1001473 selected reaction monitoring chromatogram Representation of an array of the measurements of a selectively monitored reaction versus time. PSI:MS OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time. CRM chromatogram MS MS:1001474 This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way. consecutive reaction monitoring chromatogram true OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time. PSI:MS Open Mass Spectrometry Search Algorithm was used to analyze the spectra. MS MS:1001475 OMSSA Open Mass Spectrometry Search Algorithm was used to analyze the spectra. PSI:PI X!Tandem was used to analyze the spectra. MS MS:1001476 X!Tandem X!Tandem was used to analyze the spectra. PSI:PI Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline. MS MS:1001477 SpectraST Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline. PSI:PI Mascot Parser was used to analyze the spectra. MS MS:1001478 Mascot Parser Mascot Parser was used to analyze the spectra. PSI:PI Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte. MS MS:1001479 null-terminated ASCII string Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte. PSI:MS Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger. MS MS:1001480 SCIEX TOF/TOF nativeID format Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger. PSI:MS Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database. MS MS:1001481 SCIEX TOF/TOF database Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database. PSI:MS SCIEX 5800 TOF-TOF Analyzer. MS MS:1001482 5800 TOF/TOF SCIEX 5800 TOF-TOF Analyzer. PSI:MS SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis. MS MS:1001483 SCIEX TOF/TOF Series Explorer Software SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis. PSI:MS Normalization of data point intensities. MS MS:1001484 intensity normalization Normalization of data point intensities. PSI:MS Calibration of data point m/z positions. MS MS:1001485 m/z calibration Calibration of data point m/z positions. PSI:MS Filtering out part of the data. MS MS:1001486 data filtering Filtering out part of the data. PSI:MS An algorithm for protein determination/assembly integrated into Bruker's ProteinScape. MS MS:1001487 ProteinExtractor An algorithm for protein determination/assembly integrated into Bruker's ProteinScape. PSI:MS Mascot Distiller. MS MS:1001488 Mascot Distiller Mascot Distiller. PSI:PI Mascot Integra. MS MS:1001489 Mascot Integra Mascot Integra. PSI:PI Percolator. MS MS:1001490 Percolator Percolator. PSI:PI Percolator:Q value. MS MS:1001491 percolator:Q value Percolator:Q value. PSI:PI Percolator:score. MS MS:1001492 percolator:score Percolator:score. PSI:PI Posterior error probability. MS MS:1001493 percolator:PEP Posterior error probability. PSI:PI In case no threshold was used. MS MS:1001494 no threshold In case no threshold was used. PSI:PI The SearchResultId of this peptide as SearchResult in the ProteinScape database. MS MS:1001495 ProteinScape:SearchResultId The SearchResultId of this peptide as SearchResult in the ProteinScape database. PSI:PI The SearchEventId of the SearchEvent in the ProteinScape database. MS MS:1001496 ProteinScape:SearchEventId The SearchEventId of the SearchEvent in the ProteinScape database. PSI:PI The Profound probability score stored by ProteinScape. MS MS:1001497 ProteinScape:ProfoundProbability The Profound probability score stored by ProteinScape. PSI:PI The Profound z value. MS MS:1001498 Profound:z value The Profound z value. PSI:PI The Profound cluster score. MS MS:1001499 Profound:Cluster The Profound cluster score. PSI:PI The Profound cluster rank. MS MS:1001500 Profound:ClusterRank The Profound cluster rank. PSI:PI The MSFit Mowse score. MS MS:1001501 MSFit:Mowse score The MSFit Mowse score. PSI:PI The Sonar score. MS MS:1001502 Sonar:Score The Sonar score. PSI:PI The ProteinSolver exp value stored by ProteinScape. MS MS:1001503 ProteinScape:PFFSolverExp The ProteinSolver exp value stored by ProteinScape. PSI:PI The ProteinSolver score stored by ProteinScape. MS MS:1001504 ProteinScape:PFFSolverScore The ProteinSolver score stored by ProteinScape. PSI:PI The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape. MS MS:1001505 ProteinScape:IntensityCoverage The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape. PSI:PI The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores. MS MS:1001506 ProteinScape:SequestMetaScore The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores. PSI:PI The score calculated by ProteinExtractor. MS MS:1001507 ProteinExtractor:Score The score calculated by ProteinExtractor. PSI:PI Native format defined by scanId=xsd:nonNegativeInteger. MS MS:1001508 Agilent MassHunter nativeID format Native format defined by scanId=xsd:nonNegativeInteger. PSI:PI A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer. MS MS:1001509 Agilent MassHunter format A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer. PSI:PI TSQ Vantage. MS MS:1001510 TSQ Vantage TSQ Vantage. PSI:MS Filter types which are used to filter a sequence database. MS MS:1001511 Sequence database filter types Filter types which are used to filter a sequence database. PSI:PI Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search. MS MS:1001512 Sequence database filters Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search. PSI:PI DB sequence filter pattern. MS MS:1001513 DB sequence filter pattern DB sequence filter pattern. PSI:MS DB accession filter string. MS MS:1001514 DB accession filter string DB accession filter string. PSI:MS Fragmentation information, type of product: c ion without water. MS MS:1001515 frag: c ion - H2O Fragmentation information, type of product: c ion without water. PSI:PI Fragmentation information, type of product: c ion without ammonia. MS MS:1001516 frag: c ion - NH3 Fragmentation information, type of product: c ion without ammonia. PSI:PI Fragmentation information, type of product: z ion without water. MS MS:1001517 frag: z ion - H2O Fragmentation information, type of product: z ion without water. PSI:PI Fragmentation information, type of product: z ion without ammonia. MS MS:1001518 frag: z ion - NH3 Fragmentation information, type of product: z ion without ammonia. PSI:PI Fragmentation information, type of product: x ion without water. MS MS:1001519 frag: x ion - H2O Fragmentation information, type of product: x ion without water. PSI:PI Fragmentation information, type of product: x ion without ammonia. MS MS:1001520 frag: x ion - NH3 Fragmentation information, type of product: x ion without ammonia. PSI:PI Fragmentation information, type of product: precursor ion without water. MS MS:1001521 frag: precursor ion - H2O Fragmentation information, type of product: precursor ion without water. PSI:PI Fragmentation information, type of product: precursor ion without ammonia. MS MS:1001522 frag: precursor ion - NH3 Fragmentation information, type of product: precursor ion without ammonia. PSI:PI Fragmentation information, type of product: precursor ion. MS MS:1001523 frag: precursor ion Fragmentation information, type of product: precursor ion. PSI:PI This term can describe a neutral loss m/z value that is lost from an ion. MS MS:1001524 fragment neutral loss This term can describe a neutral loss m/z value that is lost from an ion. PSI:PI This term can describe a neutral loss m/z value that is lost from an ion. MS MS:1001525 precursor neutral loss This term can describe a neutral loss m/z value that is lost from an ion. PSI:PI Native format defined by databasekey=xsd:long. MS MS:1001526 A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). spectrum from database integer nativeID format Native format defined by databasekey=xsd:long. PSI:MS Spectra from Bruker/Protagen Proteinscape database. MS MS:1001527 Proteinscape spectra Spectra from Bruker/Protagen Proteinscape database. PSI:MS Native format defined by query=xsd:nonNegativeInteger. MS MS:1001528 The spectrum (query) number in a Mascot results file, starting from 1. Mascot query number Native format defined by query=xsd:nonNegativeInteger. PSI:MS Child-terms contain information to map the results back to spectra. MS MS:1001529 spectra data details Child-terms contain information to map the results back to spectra. PSI:MS Native format defined by mzMLid=xsd:IDREF. MS MS:1001530 A unique identifier of a spectrum stored in an mzML file. mzML unique identifier Native format defined by mzMLid=xsd:IDREF. PSI:MS Native format defined by databasekey=xsd:long. MS MS:1001531 A unique identifier of a spectrum stored in a ProteinScape database. spectrum from ProteinScape database nativeID format Native format defined by databasekey=xsd:long. PSI:MS Native format defined by databasekey=xsd:string. MS MS:1001532 A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). spectrum from database string nativeID format Native format defined by databasekey=xsd:string. PSI:MS Bruker Daltonics' esquire series. MS MS:1001533 Bruker Daltonics esquire series Bruker Daltonics' esquire series. PSI:MS Bruker Daltonics' flex series. MS MS:1001534 Bruker Daltonics flex series Bruker Daltonics' flex series. PSI:MS Bruker Daltonics' BioTOF series. MS MS:1001535 Bruker Daltonics BioTOF series Bruker Daltonics' BioTOF series. PSI:MS Bruker Daltonics' micrOTOF series. MS MS:1001536 Bruker Daltonics micrOTOF series Bruker Daltonics' micrOTOF series. PSI:MS Bruker Daltonics' BioTOF: ESI TOF. MS MS:1001537 BioTOF Bruker Daltonics' BioTOF: ESI TOF. PSI:MS Bruker Daltonics' BioTOF III: ESI TOF. MS MS:1001538 BioTOF III Bruker Daltonics' BioTOF III: ESI TOF. PSI:MS Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional). MS MS:1001539 UltroTOF-Q Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional). PSI:MS Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI. MS MS:1001540 micrOTOF II Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI. PSI:MS Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI. MS MS:1001541 maXis Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI. PSI:MS Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR. MS MS:1001542 amaZon ETD Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR. PSI:MS Bruker Daltonics' microflex LRF: MALDI TOF. MS MS:1001543 microflex LRF Bruker Daltonics' microflex LRF: MALDI TOF. PSI:MS Bruker Daltonics' ultrafleXtreme: MALDI TOF. MS MS:1001544 ultrafleXtreme Bruker Daltonics' ultrafleXtreme: MALDI TOF. PSI:MS Bruker Daltonics' amaZon series. MS MS:1001545 Bruker Daltonics amaZon series Bruker Daltonics' amaZon series. PSI:MS Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. MS MS:1001546 amaZon X Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. PSI:MS Bruker Daltonics' maXis series. MS MS:1001547 Bruker Daltonics maXis series Bruker Daltonics' maXis series. PSI:MS Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. MS MS:1001548 Bruker Daltonics solarix series Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. PSI:MS Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR. MS MS:1001549 solariX Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR. PSI:MS Bruker Daltonics' microflex II: MALDI TOF. MS MS:1001550 microflex II Bruker Daltonics' microflex II: MALDI TOF. PSI:MS Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF. MS MS:1001553 autoflex II TOF/TOF Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF. PSI:MS Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF. MS MS:1001554 autoflex III TOF/TOF smartbeam Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF. PSI:MS Bruker Daltonics' autoflex: MALDI TOF. MS MS:1001555 autoflex Bruker Daltonics' autoflex: MALDI TOF. PSI:MS Bruker Daltonics' apex series. MS MS:1001556 Bruker Daltonics apex series Bruker Daltonics' apex series. PSI:MS Shimadzu Corporation software. MS MS:1001557 Shimadzu Corporation software Shimadzu Corporation software. PSI:MS Shimadzu Biotech software for data acquisition, processing, and analysis. MS MS:1001558 MALDI Solutions Shimadzu Biotech software for data acquisition, processing, and analysis. PSI:MS Native format defined by file=xsd:IDREF. MS MS:1001559 SCIEX TOF/TOF T2D nativeID format Native format defined by file=xsd:IDREF. PSI:MS Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format. MS MS:1001560 SCIEX TOF/TOF T2D format Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format. PSI:MS Scaffold analysis software. MS MS:1001561 Scaffold Scaffold analysis software. http://www.proteomesoftware.com Scaffold native ID format. MS MS:1001562 Scaffold nativeID format Scaffold native ID format. PSI:MS Source file for this mzIdentML was in SEQUEST SQT format. MS MS:1001563 SEQUEST SQT format Source file for this mzIdentML was in SEQUEST SQT format. PSI:PI Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format. MS MS:1001564 Discoverer MSF format Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format. PSI:PI Source file for this mzIdentML was in Waters IdentityE XML format. MS MS:1001565 IdentityE XML format Source file for this mzIdentML was in Waters IdentityE XML format. PSI:PI Source file for this mzIdentML was in Waters ProteinLynx XML format. MS MS:1001566 ProteinLynx XML format Source file for this mzIdentML was in Waters ProteinLynx XML format. PSI:PI Source file for this mzIdentML was in Agilent SpectrumMill directory format. MS MS:1001567 SpectrumMill directories Source file for this mzIdentML was in Agilent SpectrumMill directory format. PSI:PI Scaffold peptide probability score. MS MS:1001568 Scaffold:Peptide Probability Scaffold peptide probability score. PSI:PI Waters IdentityE peptide score. MS MS:1001569 IdentityE Score Waters IdentityE peptide score. PSI:PI ProteinLynx log likelihood score. MS MS:1001570 ProteinLynx:Log Likelihood ProteinLynx log likelihood score. PSI:PI Waters ProteinLynx Ladder score. MS MS:1001571 ProteinLynx:Ladder Score Waters ProteinLynx Ladder score. PSI:PI Spectrum mill peptide score. MS MS:1001572 SpectrumMill:Score Spectrum mill peptide score. PSI:PI SpectrumMill SPI score (%). MS MS:1001573 SpectrumMill:SPI SpectrumMill SPI score (%). PSI:PI Flag indicating to report only the spectra assigned to identified proteins. MS MS:1001574 report only spectra assigned to identified proteins Flag indicating to report only the spectra assigned to identified proteins. PSI:PI Minimum number of peptides a protein must have to be accepted. MS MS:1001575 Scaffold: Minimum Peptide Count Minimum number of peptides a protein must have to be accepted. PSI:PI Minimum protein probability a protein must have to be accepted. MS MS:1001576 Scaffold: Minimum Protein Probability Minimum protein probability a protein must have to be accepted. PSI:PI Minimum probability a peptide must have to be accepted for protein scoring. MS MS:1001577 Scaffold: Minimum Peptide Probability Minimum probability a peptide must have to be accepted for protein scoring. PSI:PI Minimum number of enzymatic termini a peptide must have to be accepted. MS MS:1001578 minimum number of enzymatic termini Minimum number of enzymatic termini a peptide must have to be accepted. PSI:PI Scaffold protein probability score. MS MS:1001579 Scaffold:Protein Probability Scaffold protein probability score. PSI:PI Discriminant score from Agilent SpectrumMill software. MS MS:1001580 SpectrumMill:Discriminant Score Discriminant score from Agilent SpectrumMill software. PSI:PI The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion. FAIMS CV MS MS:1001581 FAIMS compensation voltage The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion. PSI:MS Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data. MS MS:1001582 XCMS Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data. PSI:MS MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data. MS MS:1001583 MaxQuant MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data. PSI:MS Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF). MS MS:1001584 combined pmf + ms-ms search Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF). PSI:MS Tabb Lab software for directly comparing peptides in a database to tandem mass spectra. MS MS:1001585 MyriMatch Tabb Lab software for directly comparing peptides in a database to tandem mass spectra. PSI:MS Tabb Lab software for generating sequence tags from tandem mass spectra. MS MS:1001586 DirecTag Tabb Lab software for generating sequence tags from tandem mass spectra. PSI:MS Tabb Lab software for reconciling sequence tags to a protein database. MS MS:1001587 TagRecon Tabb Lab software for reconciling sequence tags to a protein database. PSI:MS Tabb Lab software for spectral library searches on tandem mass spectra. MS MS:1001588 Pepitome Tabb Lab software for spectral library searches on tandem mass spectra. PSI:MS Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance. Pepitome:MVH TagRecon:MVH MS MS:1001589 MyriMatch:MVH Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance. PSI:MS The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution. Pepitome:mzFidelity TagRecon:mzFidelity MS MS:1001590 MyriMatch:mzFidelity The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution. PSI:MS A representative protein selected from a set of sequence same-set or spectrum same-set proteins. MS MS:1001591 anchor protein A representative protein selected from a set of sequence same-set or spectrum same-set proteins. PSI:MS A protein with significant homology to another protein, but some distinguishing peptide matches. MS MS:1001592 family member protein A protein with significant homology to another protein, but some distinguishing peptide matches. PSI:MS TO ENDETAIL: a really generic relationship OR ortholog protein. MS MS:1001593 group member with undefined relationship OR ortholog protein TO ENDETAIL: a really generic relationship OR ortholog protein. PSI:MS A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences. MS MS:1001594 sequence same-set protein A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences. PSI:MS A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra. MS MS:1001595 spectrum same-set protein A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra. PSI:MS A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches. MS MS:1001596 sequence sub-set protein A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches. PSI:MS A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches. MS MS:1001597 spectrum sub-set protein A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches. PSI:MS A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins. MS MS:1001598 sequence subsumable protein A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins. PSI:MS A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins. MS MS:1001599 spectrum subsumable protein A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins. PSI:MS Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable). MS MS:1001600 protein inference confidence category Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable). PSI:MS OBSOLETE Name and location of the .raw file or files. MS MS:1001601 This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. ProteomeDiscoverer:Spectrum Files:Raw File names true OBSOLETE Name and location of the .raw file or files. PSI:MS OBSOLETE Path and name of the .srf (SEQUEST Result Format) file. MS MS:1001602 This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. ProteomeDiscoverer:SRF File Selector:SRF File Path true OBSOLETE Path and name of the .srf (SEQUEST Result Format) file. PSI:MS OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc). MS MS:1001603 This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead. ProteomeDiscoverer:Spectrum Selector:Ionization Source true OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc). PSI:MS OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any). MS MS:1001604 This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead. ProteomeDiscoverer:Activation Type true OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any). PSI:MS Lower retention-time limit. MS MS:1001605 ProteomeDiscoverer:Spectrum Selector:Lower RT Limit Lower retention-time limit. PSI:MS OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS). MS MS:1001606 This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead. ProteomeDiscoverer:Mass Analyzer true OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS). PSI:MS Maximum mass limit of a singly charged precursor ion. MS MS:1001607 ProteomeDiscoverer:Max Precursor Mass Maximum mass limit of a singly charged precursor ion. PSI:MS Minimum mass limit of a singly charged precursor ion. MS MS:1001608 ProteomeDiscoverer:Min Precursor Mass Minimum mass limit of a singly charged precursor ion. PSI:MS Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow. MS MS:1001609 ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow. PSI:MS OBSOLETE Level of the mass spectrum (MS2 ... MS10). MS MS:1001610 This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead. ProteomeDiscoverer:MS Order true OBSOLETE Level of the mass spectrum (MS2 ... MS10). PSI:MS OBSOLETE Polarity mode (positive or negative). MS MS:1001611 This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead. ProteomeDiscoverer:Polarity Mode true OBSOLETE Polarity mode (positive or negative). PSI:MS Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3). MS MS:1001612 ProteomeDiscoverer:Spectrum Selector:Precursor Selection Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3). PSI:MS Signal-to-Noise ratio below which peaks are removed. MS MS:1001613 ProteomeDiscoverer:SN Threshold Signal-to-Noise ratio below which peaks are removed. PSI:MS OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)). MS MS:1001614 This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead. ProteomeDiscoverer:Scan Type true OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)). PSI:MS Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value. MS MS:1001615 ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value. PSI:MS Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header. MS MS:1001616 ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header. PSI:MS Specifies the charge state of the precursor ions, if it is not defined in the scan header. MS MS:1001617 ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements Specifies the charge state of the precursor ions, if it is not defined in the scan header. PSI:MS Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header. MS MS:1001618 ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header. PSI:MS Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header. MS MS:1001619 ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header. PSI:MS Specifies the polarity of the ions monitored if it is not included in the scan header. MS MS:1001620 ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements Specifies the polarity of the ions monitored if it is not included in the scan header. PSI:MS Upper retention-time limit. MS MS:1001621 ProteomeDiscoverer:Spectrum Selector:Upper RT Limit Upper retention-time limit. PSI:MS Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors. MS MS:1001622 ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors. PSI:MS Maximum allowed mass of a neutral loss. MS MS:1001623 ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass Maximum allowed mass of a neutral loss. PSI:MS Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed. MS MS:1001624 ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed. PSI:MS Determines whether neutral loss peaks are removed from ETD and ECD spectra. MS MS:1001625 ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks Determines whether neutral loss peaks are removed from ETD and ECD spectra. PSI:MS Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra. MS MS:1001626 ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra. PSI:MS Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum. MS MS:1001627 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum. PSI:MS Determines whether precursor artifact peaks from the MS2 input spectra are removed. MS MS:1001628 ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak Determines whether precursor artifact peaks from the MS2 input spectra are removed. PSI:MS Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type. MS MS:1001629 ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type. PSI:MS Determines whether spectra from different MS order scans can be grouped together. MS MS:1001630 ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch Determines whether spectra from different MS order scans can be grouped together. PSI:MS OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species. MS MS:1001631 This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead. ProteomeDiscoverer:Spectrum Grouper:Max RT Difference true OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species. PSI:MS Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis. MS MS:1001632 ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis. PSI:MS Highest charge state that is allowed for the deconvolution of multiply charged data. MS MS:1001633 ProteomeDiscoverer:Xtract:Highest Charge Highest charge state that is allowed for the deconvolution of multiply charged data. PSI:MS OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. MS MS:1001634 This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead. ProteomeDiscoverer:Xtract:Highest MZ true OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. PSI:MS Lowest charge state that is allowed for the deconvolution of multiply charged data. MS MS:1001635 ProteomeDiscoverer:Xtract:Lowest Charge Lowest charge state that is allowed for the deconvolution of multiply charged data. PSI:MS OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. MS MS:1001636 This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead. ProteomeDiscoverer:Xtract:Lowest MZ true OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. PSI:MS Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum. MS MS:1001637 ProteomeDiscoverer:Xtract:Monoisotopic Mass Only Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum. PSI:MS Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted). MS MS:1001638 ProteomeDiscoverer:Xtract:Overlapping Remainder Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted). PSI:MS Accuracy required for a pattern fit to be considered valid. MS MS:1001639 ProteomeDiscoverer:Xtract:Required Fitting Accuracy Accuracy required for a pattern fit to be considered valid. PSI:MS Resolution at mass 400. MS MS:1001640 ProteomeDiscoverer:Xtract:Resolution At 400 Resolution at mass 400. PSI:MS Minimum charge state below which peptides are filtered out. MS MS:1001641 ProteomeDiscoverer:Lowest Charge State Minimum charge state below which peptides are filtered out. PSI:MS Maximum charge above which peptides are filtered out. MS MS:1001642 ProteomeDiscoverer:Highest Charge State Maximum charge above which peptides are filtered out. PSI:MS Determines whether spectra with scores above the threshold score are retained rather than filtered out. MS MS:1001643 ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores Determines whether spectra with scores above the threshold score are retained rather than filtered out. PSI:MS Determine dynamic post-translational modifications (PTMs). MS MS:1001644 ProteomeDiscoverer:Dynamic Modification Determine dynamic post-translational modifications (PTMs). PSI:MS Static Modification to all occurrences of a named amino acid. MS MS:1001645 ProteomeDiscoverer:Static Modification Static Modification to all occurrences of a named amino acid. PSI:MS OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database. MS MS:1001646 This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. ProteomeDiscoverer:Mascot:Decoy Search true OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database. PSI:MS Determines whether to search error-tolerant. MS MS:1001647 ProteomeDiscoverer:Mascot:Error tolerant Search Determines whether to search error-tolerant. PSI:MS Maximum size of the .mgf (Mascot Generic Format) file in MByte. MS MS:1001648 ProteomeDiscoverer:Mascot:Max MGF File Size Maximum size of the .mgf (Mascot Generic Format) file in MByte. PSI:MS URL (Uniform resource Locator) of the Mascot server. MS MS:1001649 ProteomeDiscoverer:Mascot:Mascot Server URL URL (Uniform resource Locator) of the Mascot server. PSI:MS Number of attempts to submit the Mascot search. MS MS:1001650 ProteomeDiscoverer:Mascot:Number of attempts to submit the search Number of attempts to submit the Mascot search. PSI:MS Number of attempts to submit the Mascot search. MS MS:1001651 ProteomeDiscoverer:Mascot:X Static Modification Number of attempts to submit the Mascot search. PSI:MS OBSOLETE Name of the user submitting the Mascot search. MS MS:1001652 This term was made obsolete because it's recommended to use researcher (MS:1001271) instead. ProteomeDiscoverer:Mascot:User Name true OBSOLETE Name of the user submitting the Mascot search. PSI:MS Time interval between attempts to submit a search in seconds. MS MS:1001653 ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search Time interval between attempts to submit a search in seconds. PSI:MS OBSOLETE Specifies the enzyme reagent used for protein digestion. MS MS:1001654 This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead. ProteomeDiscoverer:Enzyme Name true OBSOLETE Specifies the enzyme reagent used for protein digestion. PSI:MS OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu. MS MS:1001655 This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. ProteomeDiscoverer:Fragment Mass Tolerance true OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu. PSI:MS Type of instrument used to acquire the data in the raw file. MS MS:1001656 Mascot:Instrument Type of instrument used to acquire the data in the raw file. PSI:MS Maximum number of missed cleavage sites to consider during the digest. MS MS:1001657 ProteomeDiscoverer:Maximum Missed Cleavage Sites Maximum number of missed cleavage sites to consider during the digest. PSI:MS Minimum score in the IonScore column that each peptide must exceed in order to be reported. MS MS:1001658 ProteomeDiscoverer:Mascot:Peptide CutOff Score Minimum score in the IonScore column that each peptide must exceed in order to be reported. PSI:MS OBSOLETE Mass window for which precursor ions are considered to be the same species. MS MS:1001659 This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. ProteomeDiscoverer:Precursor Mass Tolerance true OBSOLETE Mass window for which precursor ions are considered to be the same species. PSI:MS Minimum protein score in the IonScore column that each protein must exceed in order to be reported. MS MS:1001660 ProteomeDiscoverer:Mascot:Protein CutOff Score Minimum protein score in the IonScore column that each protein must exceed in order to be reported. PSI:MS OBSOLETE Database to use in the search (configured on the Mascot server). MS MS:1001661 This term was made obsolete because it's recommended to use database name (MS:1001013) instead. ProteomeDiscoverer:Protein Database true OBSOLETE Database to use in the search (configured on the Mascot server). PSI:MS Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report. MS MS:1001662 ProteomeDiscoverer:Mascot:Protein Relevance Factor Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report. PSI:MS Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence. MS MS:1001663 ProteomeDiscoverer:Target FDR Relaxed Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence. PSI:MS Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence. MS MS:1001664 ProteomeDiscoverer:Target FDR Strict Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence. PSI:MS OBSOLETE Limits searches to entries from a particular species or group of species. MS MS:1001665 This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. ProteomeDiscoverer:Mascot:Taxonomy true OBSOLETE Limits searches to entries from a particular species or group of species. PSI:MS OBSOLETE Use average mass for the precursor. MS MS:1001666 This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead. ProteomeDiscoverer:Use Average Precursor Mass true OBSOLETE Use average mass for the precursor. PSI:MS OBSOLETE Determines whether to use MudPIT or normal scoring. MS MS:1001667 This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead. Mascot:use MudPIT scoring true OBSOLETE Determines whether to use MudPIT or normal scoring. PSI:MS Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported. MS MS:1001668 ProteomeDiscoverer:Absolute XCorr Threshold Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported. PSI:MS Determines whether to calculate a probability score for every peptide match. MS MS:1001669 ProteomeDiscoverer:SEQUEST:Calculate Probability Score Determines whether to calculate a probability score for every peptide match. PSI:MS Dynamic C-terminal modification that is used during the search. MS MS:1001670 ProteomeDiscoverer:SEQUEST:CTerminal Modification Dynamic C-terminal modification that is used during the search. PSI:MS Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained. MS MS:1001671 ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained. PSI:MS Maximum number of identical modifications that a single peptide can have. MS MS:1001672 ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide Maximum number of identical modifications that a single peptide can have. PSI:MS Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance. MS MS:1001673 ProteomeDiscoverer:Max Modifications Per Peptide Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance. PSI:MS Maximum number of peptides that are searched and scored per spectrum. MS MS:1001674 ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered Maximum number of peptides that are searched and scored per spectrum. PSI:MS Maximum number of peptide matches reported per spectrum. MS MS:1001675 ProteomeDiscoverer:Maximum Peptides Output Maximum number of peptide matches reported per spectrum. PSI:MS Maximum number of proteins that a single identified peptide can be associated with during protein assembly. MS MS:1001676 ProteomeDiscoverer:Maximum Protein References Per Peptide Maximum number of proteins that a single identified peptide can be associated with during protein assembly. PSI:MS Dynamic N-terminal modification that is used during the search. MS MS:1001677 ProteomeDiscoverer:SEQUEST:NTerminal Modification Dynamic N-terminal modification that is used during the search. PSI:MS Static modification for the C terminal of the peptide used during the search. MS MS:1001678 ProteomeDiscoverer:Peptide CTerminus Static modification for the C terminal of the peptide used during the search. PSI:MS Static modification for the N terminal of the peptide used during the search. MS MS:1001679 ProteomeDiscoverer:Peptide NTerminus Static modification for the N terminal of the peptide used during the search. PSI:MS Specifies a factor to apply to the protein score. MS MS:1001680 ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor Specifies a factor to apply to the protein score. PSI:MS Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report. MS MS:1001681 ProteomeDiscoverer:Protein Relevance Threshold Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report. PSI:MS OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database. MS MS:1001682 This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. ProteomeDiscoverer:Search Against Decoy Database true OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database. PSI:MS Use average masses for the fragments. MS MS:1001683 ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses Use average masses for the fragments. PSI:MS Determines whether a ions with neutral loss are used for spectrum matching. MS MS:1001684 ProteomeDiscoverer:Use Neutral Loss a Ions Determines whether a ions with neutral loss are used for spectrum matching. PSI:MS Determines whether b ions with neutral loss are used for spectrum matching. MS MS:1001685 ProteomeDiscoverer:Use Neutral Loss b Ions Determines whether b ions with neutral loss are used for spectrum matching. PSI:MS Determines whether y ions with neutral loss are used for spectrum matching. MS MS:1001686 ProteomeDiscoverer:Use Neutral Loss y Ions Determines whether y ions with neutral loss are used for spectrum matching. PSI:MS Determines whether z ions with neutral loss are used for spectrum matching. MS MS:1001687 ProteomeDiscoverer:Use Neutral Loss z Ions Determines whether z ions with neutral loss are used for spectrum matching. PSI:MS Uses a ions for spectrum matching with this relative factor. MS MS:1001688 ProteomeDiscoverer:SEQUEST:Weight of a Ions Uses a ions for spectrum matching with this relative factor. PSI:MS Uses b ions for spectrum matching with this relative factor. MS MS:1001689 ProteomeDiscoverer:SEQUEST:Weight of b Ions Uses b ions for spectrum matching with this relative factor. PSI:MS Uses c ions for spectrum matching with this relative factor. MS MS:1001690 ProteomeDiscoverer:SEQUEST:Weight of c Ions Uses c ions for spectrum matching with this relative factor. PSI:MS Uses c ions for spectrum matching with this relative factor. MS MS:1001691 ProteomeDiscoverer:SEQUEST:Weight of d Ions Uses c ions for spectrum matching with this relative factor. PSI:MS Uses c ions for spectrum matching with this relative factor. MS MS:1001692 ProteomeDiscoverer:SEQUEST:Weight of v Ions Uses c ions for spectrum matching with this relative factor. PSI:MS Uses c ions for spectrum matching with this relative factor. MS MS:1001693 ProteomeDiscoverer:SEQUEST:Weight of w Ions Uses c ions for spectrum matching with this relative factor. PSI:MS Uses x ions for spectrum matching with this relative factor. MS MS:1001694 ProteomeDiscoverer:SEQUEST:Weight of x Ions Uses x ions for spectrum matching with this relative factor. PSI:MS Uses y ions for spectrum matching with this relative factor. MS MS:1001695 ProteomeDiscoverer:SEQUEST:Weight of y Ions Uses y ions for spectrum matching with this relative factor. PSI:MS Uses z ions for spectrum matching with this relative factor. MS MS:1001696 ProteomeDiscoverer:SEQUEST:Weight of z Ions Uses z ions for spectrum matching with this relative factor. PSI:MS Sets a minimum protein score that each protein must exceed in order to be reported. MS MS:1001697 ProteomeDiscoverer:ZCore:Protein Score Cutoff Sets a minimum protein score that each protein must exceed in order to be reported. PSI:MS Specifies which peak to select if more than one peak is found inside the integration window. MS MS:1001698 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method Specifies which peak to select if more than one peak is found inside the integration window. PSI:MS Specifies the mass-to-charge window that enables one to look for the reporter peaks. MS MS:1001699 ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance Specifies the mass-to-charge window that enables one to look for the reporter peaks. PSI:MS Quantitation method for isobarically labeled quantitation. MS MS:1001700 ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method Quantitation method for isobarically labeled quantitation. PSI:MS OBSOLETE Format of the exported spectra (dta, mgf or mzData). MS MS:1001701 This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. ProteomeDiscoverer:Spectrum Exporter:Export Format true OBSOLETE Format of the exported spectra (dta, mgf or mzData). PSI:MS Name of the output file that contains the exported data. MS MS:1001702 ProteomeDiscoverer:Spectrum Exporter:File name Name of the output file that contains the exported data. PSI:MS Influences the modifications search. MS MS:1001703 ProteomeDiscoverer:Search Modifications Only For Identified Proteins Influences the modifications search. PSI:MS Standard high confidence XCorr parameter for charge = 1. MS MS:1001704 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 Standard high confidence XCorr parameter for charge = 1. PSI:MS Standard high confidence XCorr parameter for charge = 2. MS MS:1001705 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 Standard high confidence XCorr parameter for charge = 2. PSI:MS Standard high confidence XCorr parameter for charge = 3. MS MS:1001706 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 Standard high confidence XCorr parameter for charge = 3. PSI:MS Standard high confidence XCorr parameter for charge >= 4. MS MS:1001707 ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 Standard high confidence XCorr parameter for charge >= 4. PSI:MS Standard medium confidence XCorr parameter for charge = 1. MS MS:1001708 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 Standard medium confidence XCorr parameter for charge = 1. PSI:MS Standard medium confidence XCorr parameter for charge = 2. MS MS:1001709 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 Standard medium confidence XCorr parameter for charge = 2. PSI:MS Standard medium confidence XCorr parameter for charge = 3. MS MS:1001710 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 Standard medium confidence XCorr parameter for charge = 3. PSI:MS Standard medium confidence XCorr parameter for charge >= 4. MS MS:1001711 ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 Standard medium confidence XCorr parameter for charge >= 4. PSI:MS FT high confidence XCorr parameter for charge = 1. MS MS:1001712 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 FT high confidence XCorr parameter for charge = 1. PSI:MS FT high confidence XCorr parameter for charge = 2. MS MS:1001713 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 FT high confidence XCorr parameter for charge = 2. PSI:MS FT high confidence XCorr parameter for charge = 3. MS MS:1001714 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 FT high confidence XCorr parameter for charge = 3. PSI:MS FT high confidence XCorr parameter for charge >= 4. MS MS:1001715 ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 FT high confidence XCorr parameter for charge >= 4. PSI:MS FT medium confidence XCorr parameter for charge = 1. MS MS:1001716 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 FT medium confidence XCorr parameter for charge = 1. PSI:MS FT medium confidence XCorr parameter for charge = 2. MS MS:1001717 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 FT medium confidence XCorr parameter for charge = 2. PSI:MS FT medium confidence XCorr parameter for charge = 3. MS MS:1001718 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 FT medium confidence XCorr parameter for charge = 3. PSI:MS FT medium confidence XCorr parameter for charge >= 4. MS MS:1001719 ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 FT medium confidence XCorr parameter for charge >= 4. PSI:MS OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter. MS MS:1001720 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. ProteomeDiscoverer:1. Dynamic Modification true OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter. PSI:PI OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter. MS MS:1001721 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. ProteomeDiscoverer:2. Dynamic Modification true OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter. PSI:PI OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter. MS MS:1001722 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. ProteomeDiscoverer:3. Dynamic Modification true OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter. PSI:PI OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter. MS MS:1001723 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. ProteomeDiscoverer:4. Dynamic Modification true OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter. PSI:PI Static Modification for X. MS MS:1001724 ProteomeDiscoverer:Static Modification for X Static Modification for X. PSI:MS Minimal initial peptide probability to contribute to analysis. MS MS:1001725 ProteomeDiscoverer:Initial minimal peptide probability Minimal initial peptide probability to contribute to analysis. PSI:MS Minimum adjusted peptide probability contributing to protein probability. MS MS:1001726 ProteomeDiscoverer:Minimal peptide probability Minimum adjusted peptide probability contributing to protein probability. PSI:MS Minimum peptide weight contributing to protein probability. MS MS:1001727 ProteomeDiscoverer:Minimal peptide weight Minimum peptide weight contributing to protein probability. PSI:MS Number of spectra from 1+ precursor ions. MS MS:1001728 ProteomeDiscoverer:Number of input1 spectra Number of spectra from 1+ precursor ions. PSI:MS Number of spectra from 2+ precursor ions. MS MS:1001729 ProteomeDiscoverer:Number of input2 spectra Number of spectra from 2+ precursor ions. PSI:MS Number of spectra from 3+ precursor ions. MS MS:1001730 ProteomeDiscoverer:Number of input3 spectra Number of spectra from 3+ precursor ions. PSI:MS Number of spectra from 4+ precursor ions. MS MS:1001731 ProteomeDiscoverer:Number of input4 spectra Number of spectra from 4+ precursor ions. PSI:MS Number of spectra from 5+ precursor ions. MS MS:1001732 ProteomeDiscoverer:Number of input5 spectra Number of spectra from 5+ precursor ions. PSI:MS Total number of predicted correct protein ids (sum of probabilities). MS MS:1001733 ProteomeDiscoverer:Number of predicted correct proteins Total number of predicted correct protein ids (sum of probabilities). PSI:MS OBSOLETE Sample organism (used for annotation purposes). MS MS:1001734 This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. ProteomeDiscoverer:Organism true OBSOLETE Sample organism (used for annotation purposes). PSI:MS OBSOLETE Full path database name. MS MS:1001735 This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. ProteomeDiscoverer:Reference Database true OBSOLETE Full path database name. PSI:MS Residues considered equivalent when comparing peptides. MS MS:1001736 ProteomeDiscoverer:Residue substitution list Residues considered equivalent when comparing peptides. PSI:MS OBSOLETE File type (if not pepXML). MS MS:1001737 This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead. ProteomeDiscoverer:Source file extension true OBSOLETE File type (if not pepXML). PSI:MS OBSOLETE Input pepXML files. MS MS:1001738 This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. ProteomeDiscoverer:Source Files true OBSOLETE Input pepXML files. PSI:MS OBSOLETE Input pepXML files (old). MS MS:1001739 This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. ProteomeDiscoverer:Source Files old true OBSOLETE Input pepXML files (old). PSI:MS Windows full path for database. MS MS:1001740 ProteomeDiscoverer:WinCyg reference database Windows full path for database. PSI:MS Windows pepXML file names. MS MS:1001741 ProteomeDiscoverer:WinCyg source files Windows pepXML file names. PSI:MS Finnigan LTQ Orbitrap Velos MS. MS MS:1001742 LTQ Orbitrap Velos Finnigan LTQ Orbitrap Velos MS. PSI:MS Determines if to use A ions for spectrum matching. MS MS:1001743 ProteomeDiscoverer:Mascot:Weight of A Ions Determines if to use A ions for spectrum matching. PSI:MS Determines if to use B ions for spectrum matching. MS MS:1001744 ProteomeDiscoverer:Mascot:Weight of B Ions Determines if to use B ions for spectrum matching. PSI:MS Determines if to use C ions for spectrum matching. MS MS:1001745 ProteomeDiscoverer:Mascot:Weight of C Ions Determines if to use C ions for spectrum matching. PSI:MS Determines if to use D ions for spectrum matching. MS MS:1001746 ProteomeDiscoverer:Mascot:Weight of D Ions Determines if to use D ions for spectrum matching. PSI:MS Determines if to use V ions for spectrum matching. MS MS:1001747 ProteomeDiscoverer:Mascot:Weight of V Ions Determines if to use V ions for spectrum matching. PSI:MS Determines if to use W ions for spectrum matching. MS MS:1001748 ProteomeDiscoverer:Mascot:Weight of W Ions Determines if to use W ions for spectrum matching. PSI:MS Determines if to use X ions for spectrum matching. MS MS:1001749 ProteomeDiscoverer:Mascot:Weight of X Ions Determines if to use X ions for spectrum matching. PSI:MS Determines if to use Y ions for spectrum matching. MS MS:1001750 ProteomeDiscoverer:Mascot:Weight of Y Ions Determines if to use Y ions for spectrum matching. PSI:MS Determines if to use z ions for spectrum matching. MS MS:1001751 ProteomeDiscoverer:Mascot:Weight of Z Ions Determines if to use z ions for spectrum matching. PSI:MS Determines if to use precursor reevaluation. MS MS:1001752 ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation Determines if to use precursor reevaluation. PSI:MS Signal-to-Noise ratio below which peaks are removed (in FT mode only). MS MS:1001753 ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly Signal-to-Noise ratio below which peaks are removed (in FT mode only). PSI:MS Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches. MS MS:1001754 ProteomeDiscoverer:Mascot:Please Do not Touch this Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches. PSI:MS Phone number of the contact person or organization. MS MS:1001755 contact phone number Phone number of the contact person or organization. PSI:MS Fax number for the contact person or organization. MS MS:1001756 contact fax number Fax number for the contact person or organization. PSI:MS Toll-free phone number of the contact person or organization. MS MS:1001757 contact toll-free phone number Toll-free phone number of the contact person or organization. PSI:MS Significance threshold type used in Mascot reporting (either 'identity' or 'homology'). MS MS:1001758 Mascot:SigThresholdType Significance threshold type used in Mascot reporting (either 'identity' or 'homology'). PSI:MS Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering'). MS MS:1001759 Mascot:ProteinGrouping Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering'). PSI:MS List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'. MS MS:1001760 Percolator:features List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'. PSI:MS Waters LC-system ACQUITY UPLC. MS MS:1001761 ACQUITY UPLC Waters LC-system ACQUITY UPLC. PSI:MS Waters LC-system ACQUITY UPLC H-Class. MS MS:1001762 ACQUITY UPLC H-Class Waters LC-system ACQUITY UPLC H-Class. PSI:MS Waters LC-system ACQUITY UPLC H-Class Bio. MS MS:1001763 ACQUITY UPLC H-Class Bio Waters LC-system ACQUITY UPLC H-Class Bio. PSI:MS Waters LC-system ACQUITY UPLC I-Class. MS MS:1001764 ACQUITY UPLC I-Class Waters LC-system ACQUITY UPLC I-Class. PSI:MS Waters LC-system ACQUITY UPLC Systems with 2D Technology. MS MS:1001765 ACQUITY UPLC Systems with 2D Technology Waters LC-system ACQUITY UPLC Systems with 2D Technology. PSI:MS Waters LC-system nanoACQUITY UPLC. MS MS:1001766 nanoACQUITY UPLC Waters LC-system nanoACQUITY UPLC. PSI:MS Waters LC-system nanoACQUITY UPLC System with 1D Technology. MS MS:1001767 nanoACQUITY UPLC System with 1D Technology Waters LC-system nanoACQUITY UPLC System with 1D Technology. PSI:MS Waters LC-system nanoACQUITY UPLC with HDX Technology. MS MS:1001768 nanoACQUITY UPLC with HDX Technology Waters LC-system nanoACQUITY UPLC with HDX Technology. PSI:MS Waters LC-system TRIZAIC UPLC nanoTile. MS MS:1001769 TRIZAIC UPLC nanoTile Waters LC-system TRIZAIC UPLC nanoTile. PSI:MS Waters oa-ToF based GCT Premier. MS MS:1001770 GCT Premier Waters oa-ToF based GCT Premier. PSI:MS Waters oa-ToF based MALDI Synapt G2 HDMS. MS MS:1001771 MALDI Synapt G2 HDMS Waters oa-ToF based MALDI Synapt G2 HDMS. PSI:MS Waters oa-ToF based MALDI Synapt G2 MS. MS MS:1001772 MALDI Synapt G2 MS Waters oa-ToF based MALDI Synapt G2 MS. PSI:MS Waters oa-ToF based MALDI Synapt G2 MS. MS MS:1001773 MALDI Synapt G2-S HDMS Waters oa-ToF based MALDI Synapt G2 MS. PSI:MS Waters oa-ToF based MALDI Synapt G2-S MS. MS MS:1001774 MALDI Synapt G2-S MS Waters oa-ToF based MALDI Synapt G2-S MS. PSI:MS Waters oa-ToF based MALDI Synapt HDMS. MS MS:1001775 MALDI Synapt HDMS Waters oa-ToF based MALDI Synapt HDMS. PSI:MS Waters oa-ToF based MALDI Synapt MS. MS MS:1001776 MALDI Synapt MS Waters oa-ToF based MALDI Synapt MS. PSI:MS Waters oa-ToF based Synapt G2 HDMS. MS MS:1001777 Synapt G2 HDMS Waters oa-ToF based Synapt G2 HDMS. PSI:MS Waters oa-ToF based Synapt G2 MS. MS MS:1001778 Synapt G2 MS Waters oa-ToF based Synapt G2 MS. PSI:MS Waters oa-ToF based Synapt G2-S HDMS. MS MS:1001779 Synapt G2-S HDMS Waters oa-ToF based Synapt G2-S HDMS. PSI:MS Waters oa-ToF based Synapt G2-S MS. MS MS:1001780 Synapt G2-S MS Waters oa-ToF based Synapt G2-S MS. PSI:MS Waters oa-ToF based Synapt HDMS. MS MS:1001781 Synapt HDMS Waters oa-ToF based Synapt HDMS. PSI:MS Waters oa-ToF based Synapt MS. MS MS:1001782 Synapt MS Waters oa-ToF based Synapt MS. PSI:MS Waters oa-ToF based Xevo G2 Q-Tof. MS MS:1001783 Xevo G2 Q-Tof Waters oa-ToF based Xevo G2 Q-Tof. PSI:MS Waters oa-ToF based Xevo G2 Tof. MS MS:1001784 Xevo G2 Tof Waters oa-ToF based Xevo G2 Tof. PSI:MS Waters oa-ToF based Xevo Q-Tof. MS MS:1001785 Xevo Q-Tof Waters oa-ToF based Xevo Q-Tof. PSI:MS Waters quadrupole based 3100. MS MS:1001786 3100 Waters quadrupole based 3100. PSI:MS Waters quadrupole based Acquity SQD. MS MS:1001787 Acquity SQD Waters quadrupole based Acquity SQD. PSI:MS Waters quadrupole based Acquity TQD. MS MS:1001788 Acquity TQD Waters quadrupole based Acquity TQD. PSI:MS Waters (triple) quadrupole based Quattro micro GC. MS MS:1001789 Quattro micro GC Waters (triple) quadrupole based Quattro micro GC. PSI:MS Waters quadrupole based Xevo TQ MS. MS MS:1001790 Xevo TQ MS Waters quadrupole based Xevo TQ MS. PSI:MS Waters quadrupole based Xevo TQD. MS MS:1001791 Xevo TQD Waters quadrupole based Xevo TQD. PSI:MS Waters quadrupole based Xevo TQ-S. MS MS:1001792 Xevo TQ-S Waters quadrupole based Xevo TQ-S. PSI:MS NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences. MS MS:1001793 Mascot:PreferredTaxonomy NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences. PSI:MS Waters Empower software for liquid chromatography and mass spectrometry acquisition. MS MS:1001795 Empower Waters Empower software for liquid chromatography and mass spectrometry acquisition. PSI:MS Waters UNIFY software for liquid chromatography and mass spectrometry acquisition. MS MS:1001796 UNIFY Waters UNIFY software for liquid chromatography and mass spectrometry acquisition. PSI:MS OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide. TWIMS MS MS:1001797 This child of the former purgatory term ion mobility spectrometry was made obsolete. travelling wave ion mobility mass spectrometer true OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide. PSI:MS LECO software for data acquisition and analysis. MS MS:1001798 LECO software LECO software for data acquisition and analysis. PSI:MS Software for acquisition, processing and analysis of data for LECO instruments. MS MS:1001799 ChromaTOF software Software for acquisition, processing and analysis of data for LECO instruments. PSI:MS LECO instrument model. MS MS:1001800 LECO instrument model LECO instrument model. PSI:MS LECO high resolution time-of-flight GC mass spectrometer. MS MS:1001801 Pegasus HRT LECO high resolution time-of-flight GC mass spectrometer. PSI:MS LECO high resolution time-of-flight LC mass spectrometer. MS MS:1001802 Citius HRT LECO high resolution time-of-flight LC mass spectrometer. PSI:MS LECO GC time-of-flight mass spectrometer. MS MS:1001803 Pegasus LECO GC time-of-flight mass spectrometer. PSI:MS LECO bench-top GC time-of-flight mass spectrometer. MS MS:1001804 TruTOF LECO bench-top GC time-of-flight mass spectrometer. PSI:MS The data type of the value reported in a QuantLayer. MS MS:1001805 quantification datatype The data type of the value reported in a QuantLayer. PSI:MS Attributes describing the details of an object relevant for reporting quantification workflows or values. MS MS:1001806 quantification object attribute Attributes describing the details of an object relevant for reporting quantification workflows or values. PSI:MS Attribute describing a study variable. MS MS:1001807 study variable attribute Attribute describing a study variable. PSI:MS The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'. MS MS:1001808 technical replicate The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'. PSI:MS The study variable is 'biological replicate'. This means, the run was generated from another individual or sample. MS MS:1001809 biological replicate The study variable is 'biological replicate'. This means, the run was generated from another individual or sample. PSI:MS The experimental condition is 'case' in contrast to 'control'. MS MS:1001810 experimental condition 'case' The experimental condition is 'case' in contrast to 'control'. PSI:MS The experimental condition is 'control' in contrast to 'case'. MS MS:1001811 experimental condition 'control' The experimental condition is 'control' in contrast to 'case'. PSI:MS The experimental condition is 'disease' in contrast to 'healthy'. MS MS:1001812 experimental condition 'disease' The experimental condition is 'disease' in contrast to 'healthy'. PSI:MS The experimental condition is 'healthy' in contrast to 'disease'. MS MS:1001813 experimental condition 'healthy' The experimental condition is 'healthy' in contrast to 'disease'. PSI:MS The experimental condition is given in the value of this term. MS MS:1001814 generic experimental condition The experimental condition is given in the value of this term. PSI:MS The experimental design followed a time series design. The time point of this run is given in the value of this term. MS MS:1001815 time series, time point X The experimental design followed a time series design. The time point of this run is given in the value of this term. PSI:MS The experimental design followed a dilution series design. The concentration of this run is given in the value of this term. MS MS:1001816 dilution series, concentration X The experimental design followed a dilution series design. The concentration of this run is given in the value of this term. PSI:MS Attribute describing a raw file. MS MS:1001817 raw file attribute Attribute describing a raw file. PSI:MS The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free). MS MS:1001818 one sample run The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free). PSI:MS The raw file contains the run of two samples (e.g. SILAC, metabolic labelling). MS MS:1001819 two sample run The raw file contains the run of two samples (e.g. SILAC, metabolic labelling). PSI:MS The raw file contains the run of three samples (e.g. 3-plex SILAC). MS MS:1001820 three sample run The raw file contains the run of three samples (e.g. 3-plex SILAC). PSI:MS The raw file contains the run of four samples (e.g. 4-plex iTraq). MS MS:1001821 four sample run The raw file contains the run of four samples (e.g. 4-plex iTraq). PSI:MS The raw file contains the run of eight samples (e.g. 8-plex iTraq). MS MS:1001822 eight sample run The raw file contains the run of eight samples (e.g. 8-plex iTraq). PSI:MS Attribute describing, how raw files build a raw file group. MS MS:1001823 raw files group attribute Attribute describing, how raw files build a raw file group. PSI:MS Attribute describing, how raw files build a raw file group. MS MS:1001824 merge of runs of 1D gel bands Attribute describing, how raw files build a raw file group. PSI:MS Attribute describing a feature list. MS MS:1001825 feature list attribute Attribute describing a feature list. PSI:MS The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given. MS MS:1001826 mass trace reporting: rectangles The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given. PSI:MS The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit. MS MS:1001827 mass trace reporting: polygons The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit. PSI:MS Attribute describing a feature. MS MS:1001828 feature attribute Attribute describing a feature. PSI:MS Identifier for an SRM transition in an external document describing additional information about the transition. MS MS:1001829 SRM transition ID Identifier for an SRM transition in an external document describing additional information about the transition. PSI:MS Software from Nonlinear Dynamics for LC-MS label-free workflow. MS MS:1001830 Progenesis LC-MS Software from Nonlinear Dynamics for LC-MS label-free workflow. PSI:MS Software for SILAC workflow. MS MS:1001831 SILACAnalyzer Software for SILAC workflow. PSI:MS Quantitation software comment or any customizations to the default setup of the software. MS MS:1001832 quantitation software comment or customizations Quantitation software comment or any customizations to the default setup of the software. PSI:PI The overall workflow of this quantitation report. MS MS:1001833 quantitation analysis summary The overall workflow of this quantitation report. PSI:PI LC-MS label-free workflow (RT m/z map). MS MS:1001834 LC-MS label-free quantitation analysis LC-MS label-free workflow (RT m/z map). PSI:PI SILAC workflow (heavy, light, and sometimes medium peak). MS MS:1001835 SILAC quantitation analysis SILAC workflow (heavy, light, and sometimes medium peak). PSI:PI Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant). MS MS:1001836 spectral counting quantitation analysis Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant). PSI:PI Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range. MS MS:1001837 iTRAQ quantitation analysis Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range. PMID:15385600 PSI:PI Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). MS MS:1001838 SRM quantitation analysis Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). PSI:PI Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens). MS MS:1001839 metabolic labeling 14N / 15N quantitation analysis Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens). PSI:PI Maximum peak intensity of the LC-MS feature. MS MS:1001840 LC-MS feature intensity Maximum peak intensity of the LC-MS feature. PSI:PI Real (intensity times area) volume of the LC-MS feature. MS MS:1001841 LC-MS feature volume Real (intensity times area) volume of the LC-MS feature. PSI:PI The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting. MS MS:1001842 sequence-level spectral count The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting. PSI:PI Maximum intensity of MS1 feature. MS MS:1001843 MS1 feature maximum intensity Maximum intensity of MS1 feature. PSI:PI Area of MS1 feature. MS MS:1001844 MS1 feature area Area of MS1 feature. PSI:PI OBSOLETE Area of MS1 peak (e.g. SILAC, 15N). MS MS:1001845 This term was made obsolete because it was a duplication of MS:1001844. peak area true OBSOLETE Area of MS1 peak (e.g. SILAC, 15N). PSI:PI Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N). MS MS:1001846 isotopic pattern area Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N). PSI:PI Intensity of MS2 reporter ion (e.g. iTraq). MS MS:1001847 reporter ion intensity Intensity of MS2 reporter ion (e.g. iTraq). PSI:PI Simple ratio of two values (enumerator and denominator). MS MS:1001848 simple ratio of two values Simple ratio of two values (enumerator and denominator). PSI:PI OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values. MS MS:1001849 This term was made obsolete because the concept MatchedFeature was dropped. sum of MatchedFeature values true OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values. PSI:PI Normalized peptide value. MS MS:1001850 normalized peptide value Normalized peptide value. PSI:PI Protein quantification value calculated as sum of peptide values. MS MS:1001851 protein value: sum of peptide values Protein quantification value calculated as sum of peptide values. PSI:PI Normalized protein value. MS MS:1001852 normalized protein value Normalized protein value. PSI:PI Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis). MS MS:1001853 max fold change Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis). PSI:PI Global datatype: p-value of ANOVA of group means (e.g. Progenesis). MS MS:1001854 ANOVA p-value Global datatype: p-value of ANOVA of group means (e.g. Progenesis). PSI:PI P-value of t-Test of two groups. MS MS:1001855 t-test p-value P-value of t-Test of two groups. PSI:PI Intensity (or area) of MS2 reporter ion (e.g. iTraq). MS MS:1001856 reporter ion raw value Intensity (or area) of MS2 reporter ion (e.g. iTraq). PSI:PI Normalized value of MS2 reporter ion (e.g. iTraq). MS MS:1001857 reporter ion normalized value Normalized value of MS2 reporter ion (e.g. iTraq). PSI:PI Area of the extracted ion chromatogram (e.g. of a transition in SRM). MS MS:1001858 XIC area Area of the extracted ion chromatogram (e.g. of a transition in SRM). PSI:PI Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM). MS MS:1001859 normalized XIC area Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM). PSI:PI Protein quantification value calculated as mean of peptide ratios. MS MS:1001860 protein value: mean of peptide ratios Protein quantification value calculated as mean of peptide ratios. PSI:PI Terms used to describe types of quantification data processing. MS MS:1001861 quantification data processing Terms used to describe types of quantification data processing. PSI:MS Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting). MS MS:1001862 normalization to mean of sum of all proteins Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting). PSI:MS Normalization of protein values to approach the same distribution. MS MS:1001863 quantile normalization, proteins Normalization of protein values to approach the same distribution. PSI:MS Normalization of peptide values to approach the same distribution. MS MS:1001864 quantile normalization, peptides Normalization of peptide values to approach the same distribution. PSI:MS Automatic RT alignment of Progenesis software. MS MS:1001865 Progenesis automatic alignment Automatic RT alignment of Progenesis software. PSI:MS RT alignment of Progenesis software using automatic and manual vectors. MS MS:1001866 Progenesis manual alignment RT alignment of Progenesis software using automatic and manual vectors. PSI:MS Normalization as performed by Progenesis LC-MS. MS MS:1001867 Progenesis normalization Normalization as performed by Progenesis LC-MS. PSI:MS Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry). MS MS:1001868 distinct peptide-level q-value Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry). PSI:PI Estimation of the q-value for proteins. MS MS:1001869 protein-level q-value Estimation of the q-value for proteins. PSI:PI Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). MS MS:1001870 peptide sequence-level p-value Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). PSI:PI Estimation of the p-value for proteins. MS MS:1001871 protein-level p-value Estimation of the p-value for proteins. PSI:PI Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). MS MS:1001872 peptide sequence-level e-value Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). PSI:PI Estimation of the e-value for proteins. MS MS:1001873 protein-level e-value Estimation of the e-value for proteins. PSI:PI OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0. MS MS:1001874 This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374). FDRScore true OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0. PMID:19253293 The regular expression describing the sequence motif for a modification. MS MS:1001875 modification motif The regular expression describing the sequence motif for a modification. PSI:PI The a priori probability of a modification. MS MS:1001876 modification probability The a priori probability of a modification. PSI:PI Software for acquisition, processing and analysis of data for LECO instruments. MS MS:1001877 ChromaTOF HRT software Software for acquisition, processing and analysis of data for LECO instruments. PSI:MS Shimadzu Biotech software for data acquisition, processing, and analysis. MS MS:1001878 MALDI Solutions Microbial Identification Shimadzu Biotech software for data acquisition, processing, and analysis. PSI:MS The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation. MS MS:1001879 offset voltage The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation. PSI:MS The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum. MS MS:1001880 in-source collision-induced dissociation The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum. PSI:MS mz5 file format, modelled after mzML. MS MS:1001881 mz5 format mz5 file format, modelled after mzML. PSI:MS Attributes of the quality of a transition that affect its selection as appropriate. MS MS:1001882 transition validation attribute Attributes of the quality of a transition that affect its selection as appropriate. PSI:MS Variation of a set of signal measurements calculated as the standard deviation relative to the mean. MS MS:1001883 coefficient of variation Variation of a set of signal measurements calculated as the standard deviation relative to the mean. PSI:MS Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal. MS MS:1001884 signal-to-noise ratio Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal. PSI:MS Parameters string passed to a command-line interface software application, omitting the executable name. MS MS:1001885 command-line parameters Parameters string passed to a command-line interface software application, omitting the executable name. PSI:MS Software for data analysis of peptides and proteins. MS MS:1001886 SQID Software for data analysis of peptides and proteins. PSI:MS The SQID result 'Score'. MS MS:1001887 SQID:score The SQID result 'Score'. PSI:PI The SQID result 'deltaScore'. MS MS:1001888 SQID:deltaScore The SQID result 'deltaScore'. PSI:PI The SQID result 'protein score'. MS MS:1001889 SQID:protein score The SQID result 'protein score'. PSI:PI The data type normalised abundance for proteins produced by Progenesis LC-MS. MS MS:1001890 Progenesis:protein normalised abundance The data type normalised abundance for proteins produced by Progenesis LC-MS. PSI:MS The data type normalised abundance for peptides produced by Progenesis LC-MS. MS MS:1001891 Progenesis:peptide normalised abundance The data type normalised abundance for peptides produced by Progenesis LC-MS. PSI:MS The data type raw abundance for proteins produced by Progenesis LC-MS. MS MS:1001892 Progenesis:protein raw abundance The data type raw abundance for proteins produced by Progenesis LC-MS. PSI:MS The data type raw abundance for peptide produced by Progenesis LC-MS. MS MS:1001893 Progenesis:peptide raw abundance The data type raw abundance for peptide produced by Progenesis LC-MS. PSI:MS The data type confidence score produced by Progenesis LC-MS. MS MS:1001894 Progenesis:confidence score The data type confidence score produced by Progenesis LC-MS. PSI:MS The data type peptide count produced by Progenesis LC-MS. MS MS:1001895 Progenesis:peptide count The data type peptide count produced by Progenesis LC-MS. PSI:MS The data type feature intensity produced by Progenesis LC-MS. MS MS:1001896 Progenesis:feature intensity The data type feature intensity produced by Progenesis LC-MS. PSI:MS The data type peptide counts (unique) produced by MaxQuant. MS MS:1001897 MaxQuant:peptide counts (unique) The data type peptide counts (unique) produced by MaxQuant. PSI:MS The data type peptide counts (all) produced by MaxQuant. MS MS:1001898 MaxQuant:peptide counts (all) The data type peptide counts (all) produced by MaxQuant. PSI:MS The data type peptide counts (razor+unique) produced by MaxQuant. MS MS:1001899 MaxQuant:peptide counts (razor+unique) The data type peptide counts (razor+unique) produced by MaxQuant. PSI:MS The data type sequence length produced by MaxQuant. MS MS:1001900 MaxQuant:sequence length The data type sequence length produced by MaxQuant. PSI:MS The data type PEP (posterior error probability) produced by MaxQuant. MS MS:1001901 MaxQuant:PEP The data type PEP (posterior error probability) produced by MaxQuant. PSI:MS The data type LFQ intensity produced by MaxQuant. MS MS:1001902 MaxQuant:LFQ intensity The data type LFQ intensity produced by MaxQuant. PSI:MS The data type feature intensity produced by MaxQuant. MS MS:1001903 MaxQuant:feature intensity The data type feature intensity produced by MaxQuant. PSI:MS The data type MS2 count produced by MaxQuant. MS MS:1001904 MaxQuant:MS/MS count The data type MS2 count produced by MaxQuant. PSI:MS The emPAI value of protein abundance, produced from the emPAI algorithm. MS MS:1001905 emPAI value The emPAI value of protein abundance, produced from the emPAI algorithm. PSI:MS The APEX value of protein abundance, produced from the APEX software. MS MS:1001906 APEX value The APEX value of protein abundance, produced from the APEX software. PSI:MS The full width of a retention time window for a chromatographic peak. MS MS:1001907 retention time window width The full width of a retention time window for a chromatographic peak. PSI:MS Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source. MS MS:1001908 ISQ Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source. PSI:MS Thermo Scientific second generation Velos. MS MS:1001909 Velos Plus Thermo Scientific second generation Velos. PSI:MS Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite. MS MS:1001910 LTQ Orbitrap Elite Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite. PSI:MS Thermo Scientific Q Exactive. MS MS:1001911 Q Exactive Thermo Scientific Q Exactive. PSI:MS Thermo Scientific PinPoint SRM analysis software. MS MS:1001912 PinPoint Thermo Scientific PinPoint SRM analysis software. PSI:MS Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts. MS MS:1001913 S-lens voltage Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts. PSI:MS Python module to interface mzML Data. MS MS:1001914 pymzML Python module to interface mzML Data. PSI:MS Enzyme leukocyte elastase (EC 3.4.21.37). MS MS:1001915 leukocyte elastase Enzyme leukocyte elastase (EC 3.4.21.37). BRENDA:3.4.21.37 Enzyme proline endopeptidase (EC 3.4.21.26). MS MS:1001916 proline endopeptidase Enzyme proline endopeptidase (EC 3.4.21.26). BRENDA:3.4.21.26 Enzyme glutamyl endopeptidase (EC 3.4.21.19). Glu-C staphylococcal protease MS MS:1001917 glutamyl endopeptidase Enzyme glutamyl endopeptidase (EC 3.4.21.19). BRENDA:3.4.21.19 Chemical iodobenzoate. Cleaves after W. MS MS:1001918 2-iodobenzoate Chemical iodobenzoate. Cleaves after W. PubChem_Compound:4739928 Main identifier of a ProteomeXchange dataset. MS MS:1001919 ProteomeXchange accession number Main identifier of a ProteomeXchange dataset. PSI:PI Version number of a ProteomeXchange accession number. MS MS:1001921 ProteomeXchange accession number version number Version number of a ProteomeXchange accession number. PSI:PI DOI unique identifier of a publication. doi MS MS:1001922 Digital Object Identifier (DOI) DOI unique identifier of a publication. PSI:PI http://dx.doi.org Free text attribute that can enrich the information about an entity. MS MS:1001923 external reference keyword Free text attribute that can enrich the information about an entity. PSI:PI Keyword present in a scientific publication. MS MS:1001924 journal article keyword Keyword present in a scientific publication. PSI:PI Keyword assigned by the data submitter. MS MS:1001925 submitter keyword Keyword assigned by the data submitter. PSI:PI Keyword assigned by a data curator. MS MS:1001926 curator keyword Keyword assigned by a data curator. PSI:PI Hash assigned by the Tranche resource to an individual file. MS MS:1001927 Tranche file hash Hash assigned by the Tranche resource to an individual file. PSI:PI Hash assigned by the Tranche resource to a whole project. MS MS:1001928 Tranche project hash Hash assigned by the Tranche resource to a whole project. PSI:PI URI that allows the access to one experiment in the PRIDE database. MS MS:1001929 PRIDE experiment URI URI that allows the access to one experiment in the PRIDE database. PSI:PI URI that allows the access to one project in the PRIDE database. MS MS:1001930 PRIDE project URI URI that allows the access to one project in the PRIDE database. PSI:PI The source interface. MS MS:1001931 source interface The source interface. PSI:MS The source interface model. MS MS:1001932 source interface model The source interface model. PSI:MS The source sprayer. MS MS:1001933 source sprayer The source sprayer. PSI:MS The source sprayer type. MS MS:1001934 source sprayer type The source sprayer type. PSI:MS The source sprayer manufacturer. MS MS:1001935 source sprayer manufacturer The source sprayer manufacturer. PSI:MS The source sprayer model. MS MS:1001936 source sprayer model The source sprayer model. PSI:MS Plate where the sample solution is spotted in a MALDI or similar instrument. MS MS:1001937 sample plate Plate where the sample solution is spotted in a MALDI or similar instrument. PSI:MS The sample plate type. MS MS:1001938 sample plate type The sample plate type. PSI:MS Stainless steel plate. MS MS:1001939 stainless steel plate Stainless steel plate. PSI:MS Coated glass plate. MS MS:1001940 coated glass plate Coated glass plate. PSI:MS Whether the sprayer is fed or is loaded with sample once. MS MS:1001941 electrospray supply type Whether the sprayer is fed or is loaded with sample once. PSI:MS The sprayer is loaded with sample once. MS MS:1001942 static supply electrospray The sprayer is loaded with sample once. PSI:MS The sprayer is continuously fed with sample. MS MS:1001943 fed supply electrospray The sprayer is continuously fed with sample. PSI:MS Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts. CXP MS MS:1001944 Collision cell exit potential Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts. PSI:MS LECO nominal mass resolution time-of-flight GCxGC mass spectrometer. MS MS:1001945 Pegasus 4D LECO nominal mass resolution time-of-flight GCxGC mass spectrometer. PSI:MS PEAKS Studio software for data analysis. MS MS:1001946 PEAKS Studio PEAKS Studio software for data analysis. PSI:MS PEAKS Online software for high throughput data analysis. MS MS:1001947 PEAKS Online PEAKS Online software for high throughput data analysis. PSI:MS PEAKS Node software for high throughput data analysis. MS MS:1001948 PEAKS Node PEAKS Node software for high throughput data analysis. PSI:MS Bioinformatics Solutions Inc. Software for data processing and analysis. MS MS:1001949 BSI software Bioinformatics Solutions Inc. Software for data processing and analysis. PSI:MS The PEAKS peptide '-10lgP Score'. MS MS:1001950 PEAKS:peptideScore The PEAKS peptide '-10lgP Score'. PSI:MS The PEAKS protein '-10lgP Score'. MS MS:1001951 PEAKS:proteinScore The PEAKS protein '-10lgP Score'. PSI:MS The ZCore probability score. MS MS:1001952 ZCore:probScore The ZCore probability score. PSI:MS The source interface manufacturer. MS MS:1001953 source interface manufacturer The source interface manufacturer. PSI:MS Parameters used in the mass spectrometry acquisition. MS MS:1001954 acquisition parameter Parameters used in the mass spectrometry acquisition. PSI:MS No cleavage. MS MS:1001955 no cleavage No cleavage. PSI:MS Unspecific cleavage. MS MS:1001956 unspecific cleavage Unspecific cleavage. PSI:MS Regular expression for leukocyte elastase. MS MS:1001957 (?<=[ALIV])(? Regular expression for leukocyte elastase. PSI:PI Regular expression for proline endopeptidase. MS MS:1001958 (?<=[HKR]P)(? Regular expression for proline endopeptidase. PSI:PI Regular expression for glutamyl endopeptidase. MS MS:1001959 (?<=[^E]E) Regular expression for glutamyl endopeptidase. PSI:PI Regular expression for 2-iodobenzoate. MS MS:1001960 (?<=W) Regular expression for 2-iodobenzoate. PSI:PI Algorithm used to score the match between a spectrum and a peptide ion. MS MS:1001961 peptide spectrum match scoring algorithm Algorithm used to score the match between a spectrum and a peptide ion. PSI:MS C13 peaks to use in peak detection. MS MS:1001962 Mascot:C13 counts C13 peaks to use in peak detection. PSI:MS Weighting factor for protein list compilation by ProteinExtractor. MS MS:1001963 ProteinExtractor:Weighting Weighting factor for protein list compilation by ProteinExtractor. PSI:MS Flag indicating a second round search with Mascot. MS MS:1001964 ProteinScape:second round Mascot Flag indicating a second round search with Mascot. PSI:MS Flag indicating a second round search with Phenyx. MS MS:1001965 ProteinScape:second round Phenyx Flag indicating a second round search with Phenyx. PSI:MS The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry. MS MS:1001966 product ion mobility The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry. PSI:MS OBSOLETE The ion drift time of an MS2 product ion. MS MS:1001967 This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476). product ion drift time true OBSOLETE The ion drift time of an MS2 product ion. PSI:MS Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level. MS MS:1001968 PTM localization PSM-level statistic Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level. PSI:MS phosphoRS score for PTM site location at the PSM-level. MS MS:1001969 phosphoRS score phosphoRS score for PTM site location at the PSM-level. DOI:10.1021/pr200611n PMID:22073976 Probability that the respective isoform is correct. MS MS:1001970 phosphoRS sequence probability Probability that the respective isoform is correct. DOI:10.1021/pr200611n PMID:22073976 Estimate of the probability that the respective site is truly phosphorylated. MS MS:1001971 phosphoRS site probability Estimate of the probability that the respective site is truly phosphorylated. DOI:10.1021/pr200611n PMID:22073976 Version of the post-translational modification scoring algorithm. MS MS:1001972 PTM scoring algorithm version Version of the post-translational modification scoring algorithm. PSI:MS DeBunker software. MS MS:1001973 DeBunker DeBunker software. PSI:MS Score specific to DeBunker. MS MS:1001974 DeBunker:score Score specific to DeBunker. PSI:MS The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value. m/z difference MS MS:1001975 delta m/z The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value. PSI:MS The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value. mass difference MS MS:1001976 delta M The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value. PSI:MS MSQuant software. MS MS:1001977 MSQuant MSQuant software. PSI:MS The PTM score from MSQuant software. MS MS:1001978 MSQuant:PTM-score The PTM score from MSQuant software. DOI:10.1021/pr900721e PMID:19888749 The PTM score from MaxQuant software. MS MS:1001979 MaxQuant:PTM Score The PTM score from MaxQuant software. PSI:MS The Phospho (STY) Probabilities from MaxQuant software. MS MS:1001980 MaxQuant:Phospho (STY) Probabilities The Phospho (STY) Probabilities from MaxQuant software. PSI:MS The Phospho (STY) Score Diffs from MaxQuant software. MS MS:1001981 MaxQuant:Phospho (STY) Score Diffs The Phospho (STY) Score Diffs from MaxQuant software. PSI:MS The P-site localization probability value from MaxQuant software. MS MS:1001982 MaxQuant:P-site localization probability The P-site localization probability value from MaxQuant software. PSI:MS The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest). MS MS:1001983 MaxQuant:PTM Delta Score The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest). PSI:MS Ascore software. MS MS:1001984 Ascore software Ascore software. PSI:MS A-score for PTM site location at the PSM-level. MS MS:1001985 Ascore A-score for PTM site location at the PSM-level. DOI:10.1038/nbt1240 PMID:16964243 H-Score for peptide phosphorylation site location. MS MS:1001986 H-Score H-Score for peptide phosphorylation site location. DOI:10.1021/pr1006813 PMID:20836569 Vacuum-drying MALDI sample preparation crystallization method. MS MS:1001987 vacuum drying MALDI sample preparation Vacuum-drying MALDI sample preparation crystallization method. PSI:MS Crushed-crystal MALDI sample preparation method. MS MS:1001988 crushed crystal MALDI sample preparation Crushed-crystal MALDI sample preparation method. PSI:MS Fast-evaporation MALDI sample preparation method. MS MS:1001989 fast evaporation MALDI sample preparation Fast-evaporation MALDI sample preparation method. DOI:10.1021/ac00091a044 Overlayer method combining features of the crushed-crystal method and the fast-evaporation method. MS MS:1001990 overlayer MALDI sample preparation Overlayer method combining features of the crushed-crystal method and the fast-evaporation method. PSI:MS Sandwich MALDI sample preparation method. MS MS:1001991 sandwich MALDI sample preparation Sandwich MALDI sample preparation method. DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4 Spin coating MALDI sample preparation method. MS MS:1001992 spin coating MALDI sample preparation Spin coating MALDI sample preparation method. DOI:10.1021/cc0500710 PMID:16283807 Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling. MS MS:1001993 quick and dirty MALDI sample preparation Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling. PSI:MS Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'. MS MS:1001994 top hat baseline reduction Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'. PSI:MS Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures. MS MS:1001995 convex hull baseline reduction Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures. PSI:MS The spectrum that will be baseline subtracted is divided into a number of segments. MS MS:1001996 median baseline reduction The spectrum that will be baseline subtracted is divided into a number of segments. PSI:MS The random noise is removed by using the undecimated wavelet transform. MS MS:1001997 wavelet transformation smoothing The random noise is removed by using the undecimated wavelet transform. DOI:10.1093/bioinformatics/btl355 PMID:16820428 It searches for known patterns in the measured spectrum. SNAP MS MS:1001998 sophisticated numerical annotation procedure It searches for known patterns in the measured spectrum. DOI:10.1021/ac951158i PMID:21619291 Normalization of areas below the curves. MS MS:1001999 area normalization Normalization of areas below the curves. PSI:MS A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID. MS MS:1002000 LIFT A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID. DOI:10.1007/s00216-003-2057-0 PMID:12830354 MS1 label-based raw feature quantitation. MS MS:1002001 MS1 label-based raw feature quantitation MS1 label-based raw feature quantitation. PSI:PI MS1 label-based peptide level quantitation. MS MS:1002002 MS1 label-based peptide level quantitation MS1 label-based peptide level quantitation. PSI:PI MS1 label-based protein level quantitation. MS MS:1002003 MS1 label-based protein level quantitation MS1 label-based protein level quantitation. PSI:PI MS1 label-based proteingroup level quantitation. MS MS:1002004 MS1 label-based proteingroup level quantitation MS1 label-based proteingroup level quantitation. PSI:PI A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys. MS MS:1002005 iRT retention time normalization standard A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys. DOI:10.1002/pmic.201100463 http://www.biognosys.ch/products/rt-kit.html The type of the transitions, e.g. target or decoy. MRM transition type MS MS:1002006 SRM transition type The type of the transitions, e.g. target or decoy. PSI:MS A transition used to target a specific compound that may be in the sample. target MRM transition MS MS:1002007 target SRM transition A transition used to target a specific compound that may be in the sample. PSI:MS A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows. decoy MRM transition MS MS:1002008 decoy SRM transition A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows. PSI:MS Quantitation analysis using an isobaric labelling workflow. MS MS:1002009 isobaric label quantitation analysis Quantitation analysis using an isobaric labelling workflow. PSI:PI Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z. MS MS:1002010 TMT quantitation analysis Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z. PMID:12713048 PSI:PI Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure. DESI MS MS:1002011 desorption electrospray ionization Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure. DOI:10.1126/science.1104404 PMID:15486296 Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score). MS MS:1002012 Mascot:PTM site assignment confidence Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score). http://www.matrixscience.com/help/pt_mods_help.html#SITE Collision energy at the start of the collision energy ramp. MS MS:1002013 collision energy ramp start Collision energy at the start of the collision energy ramp. PSI:PI Collision energy at the end of the collision energy ramp. MS MS:1002014 collision energy ramp end Collision energy at the end of the collision energy ramp. PSI:PI Spectral count peptide level quantitation. MS MS:1002015 spectral count peptide level quantitation Spectral count peptide level quantitation. PSI:PI Spectral count protein level quantitation. MS MS:1002016 spectral count protein level quantitation Spectral count protein level quantitation. PSI:PI Spectral count proteingroup level quantitation. MS MS:1002017 spectral count proteingroup level quantitation Spectral count proteingroup level quantitation. PSI:PI MS1 label-based analysis. MS MS:1002018 MS1 label-based analysis MS1 label-based analysis. PSI:PI Label-free raw feature quantitation. MS MS:1002019 label-free raw feature quantitation Label-free raw feature quantitation. PSI:PI Label-free peptide level quantitation. MS MS:1002020 label-free peptide level quantitation Label-free peptide level quantitation. PSI:PI Label-free protein level quantitation. MS MS:1002021 label-free protein level quantitation Label-free protein level quantitation. PSI:PI Label-free proteingroup level quantitation. MS MS:1002022 label-free proteingroup level quantitation Label-free proteingroup level quantitation. PSI:PI MS2 tag-based analysis. MS MS:1002023 MS2 tag-based analysis MS2 tag-based analysis. PSI:PI MS2 tag-based feature level quantitation. MS MS:1002024 MS2 tag-based feature level quantitation MS2 tag-based feature level quantitation. PSI:PI MS2 tag-based peptide level quantitation. MS MS:1002025 MS2 tag-based peptide level quantitation MS2 tag-based peptide level quantitation. PSI:PI MS2 tag-based protein level quantitation. MS MS:1002026 MS2 tag-based protein level quantitation MS2 tag-based protein level quantitation. PSI:PI MS2 tag-based proteingroup level quantitation. MS MS:1002027 MS2 tag-based proteingroup level quantitation MS2 tag-based proteingroup level quantitation. PSI:PI Nucleic acid base modification (substitution, insertion or deletion). MS MS:1002028 nucleic acid base modification Nucleic acid base modification (substitution, insertion or deletion). PSI:PI Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence. MS MS:1002029 original nucleic acid sequence Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence. PSI:PI Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence. MS MS:1002030 modified nucleic acid sequence Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence. PSI:PI URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment. MS MS:1002031 PASSEL transition group browser URI URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment. PSI:PI URI that allows access to a PeptideAtlas dataset. MS MS:1002032 PeptideAtlas dataset URI URI that allows access to a PeptideAtlas dataset. PSI:PI Role of the contact person. MS MS:1002033 contact role Role of the contact person. PSI:PI The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution. MS MS:1002034 first author The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution. PSI:MS The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution. MS MS:1002035 senior author The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution. PSI:MS One of a set of authors associated with a publication or release. MS MS:1002036 co-author One of a set of authors associated with a publication or release. PSI:MS A person who submits a dataset to a repository. MS MS:1002037 dataset submitter A person who submits a dataset to a repository. PSI:MS A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy". light sample MS MS:1002038 label free sample A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy". PSI:PI Inlet properties that are associated with a value. MS MS:1002039 inlet attribute Inlet properties that are associated with a value. PSI:MS The temperature of the inlet of a mass spectrometer. MS MS:1002040 inlet temperature The temperature of the inlet of a mass spectrometer. PSI:MS The temperature of the source of a mass spectrometer. MS MS:1002041 source temperature The temperature of the source of a mass spectrometer. PSI:MS The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column. MS MS:1002042 modulation time The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column. http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429 ProteinProspector software for data acquisition and analysis. MS MS:1002043 ProteinProspector ProteinProspector software for data acquisition and analysis. PSI:PI The ProteinProspector result 'Score'. MS MS:1002044 ProteinProspector:score The ProteinProspector result 'Score'. PSI:PI The ProteinProspector result 'Expectation value'. MS MS:1002045 ProteinProspector:expectation value The ProteinProspector result 'Expectation value'. PSI:PI The original source path used for directory-based sources. MS MS:1002046 native source path The original source path used for directory-based sources. PSI:MS MS-GF software used to re-score the peptide-spectrum matches. MS MS:1002047 MS-GF MS-GF software used to re-score the peptide-spectrum matches. DOI:10.1074/mcp.M110.003731 PMID:20829449 MS-GF+ software used to analyze the spectra. MS-GFDB MS MS:1002048 MS-GF+ MS-GF+ software used to analyze the spectra. PSI:PI MS-GF raw score. MS MS:1002049 MS-GF:RawScore MS-GF raw score. PSI:PI MS-GF de novo score. MS MS:1002050 MS-GF:DeNovoScore MS-GF de novo score. PSI:PI MS-GF energy score. MS MS:1002051 MS-GF:Energy MS-GF energy score. PSI:PI MS-GF spectral E-value. MS MS:1002052 MS-GF:SpecEValue MS-GF spectral E-value. PSI:PI MS-GF E-value. MS MS:1002053 MS-GF:EValue MS-GF E-value. PSI:PI MS-GF Q-value. MS MS:1002054 MS-GF:QValue MS-GF Q-value. PSI:PI MS-GF peptide-level Q-value. MS MS:1002055 MS-GF:PepQValue MS-GF peptide-level Q-value. PSI:PI MS-GF posterior error probability. MS MS:1002056 MS-GF:PEP MS-GF posterior error probability. PSI:PI As parameter for search engine: apply the modification only at the N-terminus of a protein. MS MS:1002057 modification specificity protein N-term As parameter for search engine: apply the modification only at the N-terminus of a protein. PSI:PI As parameter for search engine: apply the modification only at the C-terminus of a protein. MS MS:1002058 modification specificity protein C-term As parameter for search engine: apply the modification only at the C-terminus of a protein. PSI:PI Microsoft Excel (can be used for spectral counting). MS MS:1002059 Microsoft Excel Microsoft Excel (can be used for spectral counting). PSI:PI The name of the UniProtKB/TrEMBL database. MS MS:1002060 database UniProtKB/TrEMBL The name of the UniProtKB/TrEMBL database. PSI:PI OBSOLETE Decoy database from a TrEMBL protein sequence database. MS MS:1002061 This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. decoy DB from UniProtKB/TrEMBL true OBSOLETE Decoy database from a TrEMBL protein sequence database. PSI:PI Metabolic labelling: natural N (mainly 14N). MS MS:1002062 metabolic labelling: natural N (mainly 14N) Metabolic labelling: natural N (mainly 14N). PSI:PI Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite. MS MS:1002063 FindPairs Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite. http://www.medizinisches-proteom-center.de/software Peptide consensus retention time. MS MS:1002064 peptide consensus RT Peptide consensus retention time. PSI:PI Peptide consensus mass/charge ratio. MS MS:1002065 peptide consensus m/z Peptide consensus mass/charge ratio. PSI:PI Method used to calculate the ratio. MS MS:1002066 ratio calculation method Method used to calculate the ratio. PSI:PI Protein quantification value calculated as median of peptide ratios. MS MS:1002067 protein value: median of peptide ratios Protein quantification value calculated as median of peptide ratios. PSI:PI Metabolic labelling: heavy N (mainly 15N). MS MS:1002068 metabolic labelling: heavy N (mainly 15N) Metabolic labelling: heavy N (mainly 15N). PSI:PI Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape. MS MS:1002069 metabolic labelling purity Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape. PSI:PI Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed. MS MS:1002070 t-test Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed. PSI:PI Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed. MS MS:1002071 ANOVA-test Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed. PSI:PI P-value as result of one of the processing steps described. Specify in the description, which processing step it was. MS MS:1002072 p-value P-value as result of one of the processing steps described. Specify in the description, which processing step it was. PSI:PI The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'. MS MS:1002073 mzIdentML format The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'. PSI:PI http://www.psidev.info/mzidentml File format containing quantification results. MS MS:1002074 quantification file format File format containing quantification results. PSI:PI The mzQuantML format for quantification data from the PSI. File extension '.mzq'. MS MS:1002075 mzQuantML format The mzQuantML format for quantification data from the PSI. File extension '.mzq'. PSI:PI http://www.psidev.info/mzquantml PAnalyzer software for getting protein evidence categories. MS MS:1002076 PAnalyzer PAnalyzer software for getting protein evidence categories. http://code.google.com/p/ehu-bio/wiki/PAnalyzer Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. MS MS:1002077 impact Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. PSI:MS OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter. MS MS:1002078 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. ProteomeDiscoverer:1. Static Modification true OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter. PSI:PI OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter. MS MS:1002079 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. ProteomeDiscoverer:2. Static Modification true OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter. PSI:PI Precursor clipping range before. MS MS:1002080 ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before Precursor clipping range before. PSI:MS Precursor clipping range after. MS MS:1002081 ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After Precursor clipping range after. PSI:MS The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column. MS MS:1002082 first column elution time The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column. PSI:MS The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column. MS MS:1002083 second column elution time The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column. PSI:MS Multidimensional chromatography modulation description. MS MS:1002084 multidimensional chromatography modulation description Multidimensional chromatography modulation description. PSI:MS Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition. MS MS:1002085 two-dimensional gas chromatography with fixed modulation time Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition. PSI:MS Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time. MS MS:1002086 two-dimensional gas chromatography with discrete modulation time steps Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time. PSI:MS Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition. MS MS:1002087 two-dimensional liquid chromatography with fixed modulation time Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition. PSI:MS Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time. MS MS:1002088 two-dimensional liquid chromatography with discrete modulation time steps Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time. PSI:MS XCorr threshold for storing peptides that do not belong to a protein. MS MS:1002089 ProteomeDiscoverer:Peptide Without Protein XCorr Threshold XCorr threshold for storing peptides that do not belong to a protein. PSI:MS Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated. MS MS:1002090 Calculate Probability Scores Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated. PSI:MS Delta Cn threshold for filtering out PSM's. MS MS:1002091 ProteomeDiscoverer:Maximum Delta Cn Delta Cn threshold for filtering out PSM's. PSI:MS Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator. MS MS:1002092 Percolator:Validation based on Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator. PSI:MS Search engine input parameter. MS MS:1002093 search engine input parameter Search engine input parameter. PSI:PI Search engine input parameter that is shared by more than one search engine. MS MS:1002094 common search engine input parameter Search engine input parameter that is shared by more than one search engine. PSI:PI Search engine input parameters specific to Mascot. MS MS:1002095 Mascot input parameter Search engine input parameters specific to Mascot. PSI:PI source:http://www.matrixscience.com/help/search_field_help.html Search engine input parameters specific to SEQUEST. MS MS:1002096 SEQUEST input parameter Search engine input parameters specific to SEQUEST. PSI:PI source:http://fields.scripps.edu/sequest/parameters.html Search engine input parameters specific to Phenyx. MS MS:1002097 Phenyx input parameter Search engine input parameters specific to Phenyx. PSI:PI Search engine input parameters specific to ProteinExtractor. MS MS:1002098 ProteinExtractor input parameter Search engine input parameters specific to ProteinExtractor. PSI:PI Search engine input parameters specific to OMSSA. MS MS:1002099 OMSSA input parameter Search engine input parameters specific to OMSSA. PSI:PI Search engine input parameters specific to ProteinScape. MS MS:1002100 ProteinScape input parameter Search engine input parameters specific to ProteinScape. PSI:PI Search engine input parameters specific to ProteomeDiscoverer. MS MS:1002101 ProteomeDiscoverer input parameter Search engine input parameters specific to ProteomeDiscoverer. PSI:PI Software input parameters. MS MS:1002103 software input parameter Software input parameters. PSI:PI Software input parameter that is shared by more than one software. MS MS:1002104 common software input parameter Software input parameter that is shared by more than one software. PSI:PI Software specific input parameter. MS MS:1002105 software specific input parameter Software specific input parameter. PSI:PI Search engine input parameters specific to Scaffold. MS MS:1002106 Scaffold input parameter Search engine input parameters specific to Scaffold. PSI:PI Search engine input parameters specific to Percolator. MS MS:1002107 Percolator input parameter Search engine input parameters specific to Percolator. PSI:PI Indicates that a higher score is better. MS MS:1002108 higher score better Indicates that a higher score is better. PSI:PI Indicates that a lower score is better. MS MS:1002109 lower score better Indicates that a lower score is better. PSI:PI Attribute describing an assay. MS MS:1002110 assay attribute Attribute describing an assay. PSI:PI Attribute describing an assay label. MS MS:1002111 assay label attribute Attribute describing an assay label. PSI:PI Attribute describing a protein group list. MS MS:1002112 protein group list attribute Attribute describing a protein group list. PSI:PI Attribute describing a protein group. MS MS:1002113 protein group attribute Attribute describing a protein group. PSI:PI Attribute describing a protein list. MS MS:1002114 protein list attribute Attribute describing a protein list. PSI:PI Attribute describing a peptide consensus list. MS MS:1002115 peptide consensus list attribute Attribute describing a peptide consensus list. PSI:PI Attribute describing a peptide consensus. MS MS:1002116 peptide consensus attribute Attribute describing a peptide consensus. PSI:PI Attribute describing a small molecule list. MS MS:1002117 small molecule list attribute Attribute describing a small molecule list. PSI:PI Attribute describing a small molecule. MS MS:1002118 small molecule attribute Attribute describing a small molecule. PSI:PI Attribute describing a small molecule modification. MS MS:1002119 small molecule modification attribute Attribute describing a small molecule modification. PSI:PI The name for identifying an experiment. MS MS:1002120 experiment name The name for identifying an experiment. PSI:PI Dummy decribing a spectral count feature. MS MS:1002121 spectral count feature Dummy decribing a spectral count feature. PSI:PI FeatureList of spectral counts. MS MS:1002122 counts reporting FeatureList of spectral counts. PSI:PI X-Tracker generic tool for quantitative proteomics. MS MS:1002123 x-Tracker X-Tracker generic tool for quantitative proteomics. https://bessantlab.org/software/x-tracker/ ProteoSuite software for the analysis of quantitative proteomics data. MS MS:1002124 ProteoSuite ProteoSuite software for the analysis of quantitative proteomics data. DOI:10.1089/omi.2012.0022 PMID:22804616 http://www.proteosuite.org/ OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. MS MS:1002125 This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375). combined FDRScore true OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. PMID:19253293 The name of the UniProtKB knowledgebase. MS MS:1002126 database UniProtKB The name of the UniProtKB knowledgebase. PSI:PI Attribute describing an identification file. MS MS:1002127 identification file attribute Attribute describing an identification file. PSI:PI Attribute describing a method file format. MS MS:1002128 method file format Attribute describing a method file format. PSI:PI Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment. MS MS:1002129 ITRAQAnalyzer Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment. http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html Attribute describing an identification file format. MS MS:1002130 identification file format Attribute describing an identification file format. PSI:PI Noise filter component of the TOPP software. MS MS:1002131 TOPP noise filter Noise filter component of the TOPP software. PSI:PI Removes noise from profile spectra by using a gaussian smoothing. MS MS:1002132 TOPP NoiseFilterGaussian Removes noise from profile spectra by using a gaussian smoothing. PSI:PI Removes noise from profile spectra by using a Savitzky-Golay smoothing. MS MS:1002133 TOPP NoiseFilterSGolay Removes noise from profile spectra by using a Savitzky-Golay smoothing. PSI:PI Peak picker component of the TOPP software. MS MS:1002134 TOPP peak picker Peak picker component of the TOPP software. PSI:PI Finds mass spectrometric peaks in high-resoluted profile mass spectra. MS MS:1002135 TOPP PeakPickerHiRes Finds mass spectrometric peaks in high-resoluted profile mass spectra. PSI:PI Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra. MS MS:1002136 TOPP PeakPickerWavelet Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra. PSI:PI Spectra filter component of the TOPP software. MS MS:1002137 TOPP spectra filter Spectra filter component of the TOPP software. PSI:PI Applies a Bern et al normalization to peak spectra. MS MS:1002138 TOPP SpectraFilterBernNorm Applies a Bern et al normalization to peak spectra. DOI:10.1093/bioinformatics/bth947 PMID:15262780 Applies a filter to peak spectra for marked peaks. MS MS:1002139 TOPP SpectraFilterMarkerMower Applies a filter to peak spectra for marked peaks. PSI:PI Retains the n largest peaks of a peak spectra. MS MS:1002140 TOPP SpectraFilterNLargest Retains the n largest peaks of a peak spectra. PSI:PI Applies a TIC/maximal intensity normalization to peak spectra. MS MS:1002141 TOPP SpectraFilterNormalizer Applies a TIC/maximal intensity normalization to peak spectra. PSI:PI Filters putative unfragmented precursor ions from tandem spectra. MS MS:1002142 TOPP SpectraFilterParentPeakMower Filters putative unfragmented precursor ions from tandem spectra. PSI:PI Applies a filter to peak spectra after intensity scaling according to rank. MS MS:1002143 TOPP SpectraFilterScaler Applies a filter to peak spectra after intensity scaling according to rank. PSI:PI Applies a filter to peak spectra after intensity scaling to the square root. MS MS:1002144 TOPP SpectraFilterSqrtMower Applies a filter to peak spectra after intensity scaling to the square root. PSI:PI Applies a filter of peaks below a given threshold to peak spectra. MS MS:1002145 TOPP SpectraFilterThresholdMower Applies a filter of peaks below a given threshold to peak spectra. PSI:PI Applies a filter of the largest peaks in a sliding window over a peak spectrum. MS MS:1002146 TOPP SpectraFilterWindowMower Applies a filter of the largest peaks in a sliding window over a peak spectrum. PSI:PI Map aligner component of the TOPP software. MS MS:1002147 TOPP map aligner Map aligner component of the TOPP software. PSI:PI Corrects retention time distortions between maps based on common peptide identifications. MS MS:1002148 TOPP MapAlignerIdentification Corrects retention time distortions between maps based on common peptide identifications. PSI:PI Corrects retention time distortions between maps using a pose clustering approach. MS MS:1002149 TOPP MapAlignerPoseClustering Corrects retention time distortions between maps using a pose clustering approach. PSI:PI Corrects retention time distortions between maps by spectrum alignment. MS MS:1002150 TOPP MapAlignerSpectrum Corrects retention time distortions between maps by spectrum alignment. PSI:PI Attribute describing the data type of the numerator of a ratio. MS MS:1002151 numerator data type attribute Attribute describing the data type of the numerator of a ratio. PSI:PI Attribute describing the data type of the denominator of a ratio. MS MS:1002152 denominator data type attribute Attribute describing the data type of the denominator of a ratio. PSI:PI The number of spectra identified for this protein in spectral counting. MS MS:1002153 protein level PSM counts The number of spectra identified for this protein in spectral counting. PSI:PI Extracts spectra of an MS run file to several files in DTA format. MS MS:1002154 TOPP DTAExtractor Extracts spectra of an MS run file to several files in DTA format. PSI:PI Merges several protein/peptide identification files into one file. MS MS:1002155 TOPP IDMerger Merges several protein/peptide identification files into one file. PSI:PI Converts identification engine file formats. MS MS:1002156 TOPP IDFileConverter Converts identification engine file formats. PSI:PI Merges spectra from an LC/MS map, either by precursor or by RT blocks. MS MS:1002157 TOPP SpectraMerger Merges spectra from an LC/MS map, either by precursor or by RT blocks. PSI:PI Exports various XML formats to an mzTab file. MS MS:1002158 TOPP MzTabExporter Exports various XML formats to an mzTab file. PSI:PI Annotates mass traces in centroided LC/MS maps. MS MS:1002159 TOPP MassTraceExtractor Annotates mass traces in centroided LC/MS maps. PSI:PI Correct the precursor entries of tandem MS scans. MS MS:1002160 TOPP PrecursorMassCorrector Correct the precursor entries of tandem MS scans. PSI:PI Performs precursor mz correction on centroided high resolution data. MS MS:1002161 TOPP HighResPrecursorMassCorrector Performs precursor mz correction on centroided high resolution data. PSI:PI Computes an additive series to quantify a peptide in a set of samples. MS MS:1002162 TOPP AdditiveSeries Computes an additive series to quantify a peptide in a set of samples. PSI:PI Decharges and merges different feature charge variants of the same chemical entity. MS MS:1002163 TOPP Decharger Decharges and merges different feature charge variants of the same chemical entity. PSI:PI Quantifies signals at given positions in (raw or picked) LC/MS maps. MS MS:1002164 TOPP EICExtractor Quantifies signals at given positions in (raw or picked) LC/MS maps. PSI:PI Feature finder component of the TOPP software. MS MS:1002165 TOPP feature finder Feature finder component of the TOPP software. PSI:PI Detects two-dimensional features in centroided LC-MS data. MS MS:1002166 TOPP FeatureFinderCentroided Detects two-dimensional features in centroided LC-MS data. PSI:PI Detects two-dimensional features in uncentroided LC-MS data. MS MS:1002167 TOPP FeatureFinderRaw Detects two-dimensional features in uncentroided LC-MS data. PSI:PI Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm. MS MS:1002168 TOPP FeatureFinderIsotopeWavelet Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm. PSI:PI Detects two-dimensional features in centroided LC-MS data of metabolites. MS MS:1002169 TOPP FeatureFinderMetabo Detects two-dimensional features in centroided LC-MS data of metabolites. PSI:PI Quantifies features LC-MS/MS MRM data. MS MS:1002170 TOPP FeatureFinderMRM Quantifies features LC-MS/MS MRM data. PSI:PI Computes protein abundances from annotated feature/consensus maps. MS MS:1002171 TOPP ProteinQuantifier Computes protein abundances from annotated feature/consensus maps. PSI:PI Normalizes maps of one consensus XML file (after linking). MS MS:1002172 TOPP ConsensusMapNormalizer Normalizes maps of one consensus XML file (after linking). PSI:PI Applies retention time transformations to maps. MS MS:1002173 TOPP MapRTTransformer Applies retention time transformations to maps. PSI:PI Feature linker component of the TOPP software. MS MS:1002174 TOPP feature linker Feature linker component of the TOPP software. PSI:PI Groups corresponding isotope-labeled features in a feature map. MS MS:1002175 TOPP FeatureLinkerLabeled Groups corresponding isotope-labeled features in a feature map. PSI:PI Groups corresponding features from multiple maps. MS MS:1002176 TOPP FeatureLinkerUnlabeled Groups corresponding features from multiple maps. PSI:PI Groups corresponding features from multiple maps using a quality threshold clustering approach. MS MS:1002177 TOPP FeatureLinkerUnlabeledQT Groups corresponding features from multiple maps using a quality threshold clustering approach. PSI:PI Performs a peptide/protein identification with the CompNovo engine. MS MS:1002178 TOPP CompNovo Performs a peptide/protein identification with the CompNovo engine. PSI:PI Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode. MS MS:1002179 TOPP CompNovoCID Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode. PSI:PI Software adaptor to an external program in the TOPP software. MS MS:1002180 TOPP software adaptor Software adaptor to an external program in the TOPP software. PSI:PI Identifies MS2 spectra using the external program Inspect. MS MS:1002181 TOPP InspectAdapter Identifies MS2 spectra using the external program Inspect. PSI:PI Identifies MS2 spectra using the external program Mascot. MS MS:1002182 TOPP MascotAdapter Identifies MS2 spectra using the external program Mascot. PSI:PI Identifies MS2 spectra using the online version of the external program Mascot. MS MS:1002183 TOPP MascotAdapterOnline Identifies MS2 spectra using the online version of the external program Mascot. PSI:PI Identifies MS2 spectra using the external program OMSSA. MS MS:1002184 TOPP OMSSAAdapter Identifies MS2 spectra using the external program OMSSA. PSI:PI Identifies MS2 spectra using the external program PepNovo. MS MS:1002185 TOPP PepNovoAdapter Identifies MS2 spectra using the external program PepNovo. PSI:PI Identifies MS2 spectra using the external program XTandem. MS MS:1002186 TOPP XTandemAdapter Identifies MS2 spectra using the external program XTandem. PSI:PI Identifies peptide MS2 spectra by spectral matching with a searchable spectral library. MS MS:1002187 TOPP SpecLibSearcher Identifies peptide MS2 spectra by spectral matching with a searchable spectral library. PSI:PI Computes a consensus identification from peptide identifications of several identification engines. MS MS:1002188 TOPP ConsensusID Computes a consensus identification from peptide identifications of several identification engines. PSI:PI Resolves ambiguous annotations of features with peptide identifications. MS MS:1002189 TOPP IDConflictResolver Resolves ambiguous annotations of features with peptide identifications. PSI:PI Filters results from protein or peptide identification engines based on different criteria. MS MS:1002190 TOPP IDFilter Filters results from protein or peptide identification engines based on different criteria. PSI:PI Assigns protein/peptide identifications to feature or consensus features. MS MS:1002191 TOPP IDMapper Assigns protein/peptide identifications to feature or consensus features. PSI:PI Estimates posterior error probabilities using a mixture model. MS MS:1002192 TOPP IDPosteriorErrorProbability Estimates posterior error probabilities using a mixture model. PSI:PI Calibrate Retention times of peptide hits to standards. MS MS:1002193 TOPP IDRTCalibration Calibrate Retention times of peptide hits to standards. PSI:PI Refreshes the protein references for all peptide hits. MS MS:1002194 TOPP PeptideIndexer Refreshes the protein references for all peptide hits. PSI:PI A tool for precursor ion selection based on identification results. MS MS:1002195 TOPP PrecursorIonSelector A tool for precursor ion selection based on identification results. PSI:PI MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML). MS MS:1002196 TOPP MRMMapper MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML). PSI:PI OpenSwath component of the TOPP software. MS MS:1002197 TOPP OpenSwath component OpenSwath component of the TOPP software. PSI:PI Picks peaks and finds features in an SRM experiment. MS MS:1002198 TOPP OpenSwathAnalyzer Picks peaks and finds features in an SRM experiment. PSI:PI Extract chromatograms (XIC) from a MS2 map file. MS MS:1002199 TOPP OpenSwathChromatogramExtractor Extract chromatograms (XIC) from a MS2 map file. PSI:PI Generates decoys according to different models for a specific TraML. MS MS:1002200 TOPP OpenSwathDecoyGenerator Generates decoys according to different models for a specific TraML. PSI:PI Converts a featureXML to a mProphet tsv (tab separated values). MS MS:1002201 TOPP OpenSwathFeatureXMLToTSV Converts a featureXML to a mProphet tsv (tab separated values). PSI:PI Generates a transformation file for retention time space into normalized space. MS MS:1002202 TOPP OpenSwathRTNormalizer Generates a transformation file for retention time space into normalized space. PSI:PI Infer proteins from a list of (high-confidence) peptides. MS MS:1002203 TOPP ProteinInference Infer proteins from a list of (high-confidence) peptides. PSI:PI Estimates the false discovery rate on peptide and protein level using decoy searches. MS MS:1002204 TOPP FalseDiscoveryRate Estimates the false discovery rate on peptide and protein level using decoy searches. PSI:PI Converts, filters, and processes mass spectrometry data in variety of formats. MS MS:1002205 ProteoWizard msconvert Converts, filters, and processes mass spectrometry data in variety of formats. PSI:MS Converts, filters, and processes identifications from shotgun proteomics experiments. MS MS:1002206 ProteoWizard idconvert Converts, filters, and processes identifications from shotgun proteomics experiments. PSI:MS Filters and processes protein sequence databases. MS MS:1002207 ProteoWizard chainsaw Filters and processes protein sequence databases. PSI:MS Filters, processes, and displays mass spectrometry data in a variety of ways. MS MS:1002208 ProteoWizard msaccess Filters, processes, and displays mass spectrometry data in a variety of ways. PSI:MS An interactive GUI application to view and filter mass spectrometry data in a variety of formats. MS MS:1002209 ProteoWizard SeeMS An interactive GUI application to view and filter mass spectrometry data in a variety of formats. PSI:MS A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data. MS MS:1002210 IsobariQ A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data. DOI:10.1021/pr1009977 PMID:21067241 http://folk.uio.no/magnusar/isobariq The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. MS MS:1002211 Variance stabilizing normalization The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. PMID:16646781 Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric. MS MS:1002212 IPTL quantitation analysis Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric. PMID:19655813 PSI:PI A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum). MS MS:1002213 PAnalyzer:conclusive protein A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum). PSI:PI A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum). MS MS:1002214 PAnalyzer:indistinguishable protein A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum). PSI:PI A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). MS MS:1002215 PAnalyzer:non-conclusive protein A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). PSI:PI A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). MS MS:1002216 PAnalyzer:ambiguous group member A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). PSI:PI A putative identified peptide issued from a decoy sequence database. MS MS:1002217 decoy peptide A putative identified peptide issued from a decoy sequence database. PSI:PI Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion. MS MS:1002218 percent collision energy ramp start Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion. PSI:PI Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion. MS MS:1002219 percent collision energy ramp end Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion. PSI:PI A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database. MS MS:1002220 MRMaid A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database. PSI:PI Score in MRMaid to indicate the expected performance of the peptide in SRM. MS MS:1002221 MRMaid:peptide score Score in MRMaid to indicate the expected performance of the peptide in SRM. PSI:PI Attribute associated with a SRM transition. MS MS:1002222 SRM transition attribute Attribute associated with a SRM transition. PSI:MS Probability of detecting precursor when parent protein is present. MS MS:1002223 precursor ion detection probability Probability of detecting precursor when parent protein is present. PSI:PI Probability of detecting product ion when precursor ion is present. MS MS:1002224 product ion detection probability Probability of detecting product ion when precursor ion is present. PSI:PI Average value of product ion intensity in a collection of identified spectra. MS MS:1002225 average product ion intensity Average value of product ion intensity in a collection of identified spectra. PSI:PI Standard deviation of product ion intensity in a collection of identified spectra. MS MS:1002226 product ion intensity standard deviation Standard deviation of product ion intensity in a collection of identified spectra. PSI:PI The number of times the specific product ion has been observed in a series of SRM experiments. MS MS:1002227 number of product ion observations The number of times the specific product ion has been observed in a series of SRM experiments. PSI:PI The number of times the specific precursor ion has been observed in a series of SRM experiments. MS MS:1002228 number of precursor ion observations The number of times the specific precursor ion has been observed in a series of SRM experiments. PSI:PI Calculated relaxed significance when performing a decoy search for high-confidence peptides. MS MS:1002229 ProteomeDiscoverer:Mascot:Significance Middle Calculated relaxed significance when performing a decoy search for high-confidence peptides. PSI:PI Calculated relaxed significance when performing a decoy search for medium-confidence peptides. MS MS:1002230 ProteomeDiscoverer:Mascot:Significance High Calculated relaxed significance when performing a decoy search for medium-confidence peptides. PSI:PI ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12}). MS MS:1002231 regular expressions for a GUID ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12}). PSI:PI The default FDR calculator as globally unique identifier (GUID). MS MS:1002232 ProteomeDiscoverer:Default FDR calculator The default FDR calculator as globally unique identifier (GUID). PSI:PI Flag indicating if low-resolution spectra are taken into consideration. MS MS:1002233 ProteomeDiscoverer:SEQUEST:Low resolution spectra contained Flag indicating if low-resolution spectra are taken into consideration. PSI:PI Mass-to-charge ratio of a precursor ion selected for fragmentation. MS selected ion m/z MS:1002234 selected precursor m/z Mass-to-charge ratio of a precursor ion selected for fragmentation. PSI:PI A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores. MS MS:1002235 ProteoGrouper:PDH score A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores. PSI:PI A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides. MS MS:1002236 ProteoGrouper:PAG score A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides. PSI:PI A library of Java routines for manipulating mzIdentML files. MS MS:1002237 mzidLib A library of Java routines for manipulating mzIdentML files. PSI:PI A converter for OMSSA OMX to mzIdentML. MS MS:1002238 mzidLib:Omssa2Mzid A converter for OMSSA OMX to mzIdentML. PSI:PI A converter for Tandem XML to mzIdentML. MS MS:1002239 mzidLib:Tandem2Mzid A converter for Tandem XML to mzIdentML. PSI:PI A converter for CSV files (following OMSSA CSV style) to mzIdentML. MS MS:1002240 mzidLib:Csv2Mzid A converter for CSV files (following OMSSA CSV style) to mzIdentML. PSI:PI A generic and parameterizable protein inference algorithm for mzIdentML files. MS MS:1002241 mzidLib:ProteoGrouper A generic and parameterizable protein inference algorithm for mzIdentML files. PSI:PI A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files. MS MS:1002242 mzidLib:Thresholder A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files. PSI:PI A routine for adding emPAI quantitative values to an mzIdentML file. MS MS:1002243 mzidLib:Perform emPAI on mzid A routine for adding emPAI quantitative values to an mzIdentML file. PSI:PI A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search. MS MS:1002244 mzidLib:FalseDiscoveryRate A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search. PSI:PI A tool for converting mzIdentML files to CSV format. MS MS:1002245 mzidLib:Mzidentml2Csv A tool for converting mzIdentML files to CSV format. PSI:PI A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file. MS MS:1002246 mzidLib:CombineSearchEngines A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file. PMID:19253293 A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files. MS MS:1002247 mzidLib:InsertMetaDataFromFasta A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files. PSI:PI The SEQUEST result 'SpScore'. MS MS:1002248 SEQUEST:spscore The SEQUEST result 'SpScore'. PSI:PI The SEQUEST result 'SpRank'. MS MS:1002249 SEQUEST:sprank The SEQUEST result 'SpRank'. PSI:PI The SEQUEST result 'DeltaCnStar'. MS MS:1002250 SEQUEST:deltacnstar The SEQUEST result 'DeltaCnStar'. PSI:PI Comet open-source sequence search engine developed at the University of Washington. MS MS:1002251 Comet Comet open-source sequence search engine developed at the University of Washington. PMID:23148064 The Comet result 'XCorr'. MS MS:1002252 Comet:xcorr The Comet result 'XCorr'. PSI:PI The Comet result 'DeltaCn'. MS MS:1002253 Comet:deltacn The Comet result 'DeltaCn'. PSI:PI The Comet result 'DeltaCnStar'. MS MS:1002254 Comet:deltacnstar The Comet result 'DeltaCnStar'. PSI:PI The Comet result 'SpScore'. MS MS:1002255 Comet:spscore The Comet result 'SpScore'. PSI:PI The Comet result 'SpRank'. MS MS:1002256 Comet:sprank The Comet result 'SpRank'. PSI:PI The Comet result 'Expectation value'. MS MS:1002257 Comet:expectation value The Comet result 'Expectation value'. PSI:PI The Comet result 'Matched Ions'. MS MS:1002258 Comet:matched ions The Comet result 'Matched Ions'. PSI:PI The Comet result 'Total Ions'. MS MS:1002259 Comet:total ions The Comet result 'Total Ions'. PSI:PI False-discovery rate threshold for peptide-spectrum matches. MS MS:1002260 PSM:FDR threshold False-discovery rate threshold for peptide-spectrum matches. PSI:PI Byonic search engine from Protein Metrics. MS MS:1002261 Byonic Byonic search engine from Protein Metrics. PMID:23255153 The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct. MS MS:1002262 Byonic:Score The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct. PSI:PI The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct. MS MS:1002263 Byonic:Delta Score The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct. PSI:PI The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct. MS MS:1002264 Byonic:DeltaMod Score The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct. PSI:PI Byonic posterior error probability. MS MS:1002265 Byonic:PEP Byonic posterior error probability. PSI:PI The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism. MS MS:1002266 Byonic:Peptide LogProb The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism. PSI:PI The log p-value of the protein. MS MS:1002267 Byonic:Protein LogProb The log p-value of the protein. PSI:PI Best (most negative) log p-value of an individual PSM. MS MS:1002268 Byonic:Best LogProb Best (most negative) log p-value of an individual PSM. PSI:PI Best (largest) Byonic score of a PSM. MS MS:1002269 Byonic:Best Score Best (largest) Byonic score of a PSM. PSI:PI A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure. MS MS:1002270 chromatography separation A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure. PSI:MS Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. MS MS:1002271 liquid chromatography separation Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. PSI:MS Gas chromatography (GC) is a separation technique in which the mobile phase is a gas. MS MS:1002272 gas chromatography separation Gas chromatography (GC) is a separation technique in which the mobile phase is a gas. PSI:MS Detector potential difference in volts. MS MS:1002273 detector potential Detector potential difference in volts. PSI:MS Waters quadrupole based SQ Detector 2. MS MS:1002274 SQ Detector 2 Waters quadrupole based SQ Detector 2. PSI:MS Waters oa-ToF based Xevo G2-S Tof. MS MS:1002275 Xevo G2-S Tof Waters oa-ToF based Xevo G2-S Tof. PSI:MS Waters oa-ToF based Xevo G2-S QTof. MS MS:1002276 Xevo G2-S QTof Waters oa-ToF based Xevo G2-S QTof. PSI:MS Waters AutoSpec Premier magnetic sector instrument. MS MS:1002277 AutoSpec Premier Waters AutoSpec Premier magnetic sector instrument. PSI:MS LECO nominal mass resolution time-of-flight GC mass spectrometer. MS MS:1002278 Pegasus III LECO nominal mass resolution time-of-flight GC mass spectrometer. PSI:MS Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. MS MS:1002279 maXis 4G Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. PSI:MS Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. MS MS:1002280 compact Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. PSI:MS Selected Reaction Monitoring feature level quantitation. MS MS:1002281 SRM feature level quantitation Selected Reaction Monitoring feature level quantitation. PSI:PI Selected Reaction Monitoring peptide level quantitation. MS MS:1002282 SRM peptide level quantitation Selected Reaction Monitoring peptide level quantitation. PSI:PI Selected Reaction Monitoring protein level quantitation. MS MS:1002283 SRM protein level quantitation Selected Reaction Monitoring protein level quantitation. PSI:PI Selected Reaction Monitoring proteingroup level quantitation. MS MS:1002284 SRM proteingroup level quantitation Selected Reaction Monitoring proteingroup level quantitation. PSI:PI A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology. TPP MS MS:1002285 Trans-Proteomic Pipeline A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology. PSI:PI A software program that is a component of the Trans-Proteomic Pipeline. MS MS:1002286 Trans-Proteomic Pipeline software A software program that is a component of the Trans-Proteomic Pipeline. PSI:PI A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format. MS MS:1002287 PeptideProphet A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format. PMID:12403597 PMID:23176103 A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format. InterProphet MS MS:1002288 iProphet A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format. PMID:21876204 A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format. MS MS:1002289 ProteinProphet A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format. PMID:14632076 A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. MS MS:1002290 XPRESS A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. PSI:PI A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc. MS MS:1002291 Libra A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc. PSI:PI A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites. MS MS:1002292 PTMProphet A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites. PSI:PI Bruker Daltonics' SCION series. MS MS:1002293 Bruker Daltonics SCION series Bruker Daltonics' SCION series. PSI:MS Bruker Daltonics' EVOQ series. MS MS:1002294 Bruker Daltonics EVOQ series Bruker Daltonics' EVOQ series. PSI:MS Bruker Daltonics' SCION SQ: GC-single quadrupole. MS MS:1002295 SCION SQ Bruker Daltonics' SCION SQ: GC-single quadrupole. PSI:MS Bruker Daltonics' SCION TQ: GC-triple quadrupole. MS MS:1002296 SCION TQ Bruker Daltonics' SCION TQ: GC-triple quadrupole. PSI:MS Bruker Daltonics' EVOQ Elite: LC-triple quadrupole. MS MS:1002297 EVOQ Elite Bruker Daltonics' EVOQ Elite: LC-triple quadrupole. PSI:MS Bruker Daltonics' EVOQ Qube: LC-triple quadrupole. MS MS:1002298 EVOQ Qube Bruker Daltonics' EVOQ Qube: LC-triple quadrupole. PSI:MS Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. MS MS:1002299 micrOTOF-Q III Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. PSI:MS Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray. MS MS:1002300 amaZon Speed ETD Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray. PSI:MS Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. MS MS:1002301 amaZon Speed Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. PSI:MS Bruker Container raw file format. MS MS:1002302 Bruker Container format Bruker Container raw file format. PSI:MS Native identifier (UUID). MS MS:1002303 Bruker Container nativeID format Native identifier (UUID). PSI:MS Domain range of a numerical value. MS MS:1002304 domain range Domain range of a numerical value. PSI:PI Value range for probabilities. MS MS:1002305 value between 0 and 1 inclusive Value range for probabilities. PSI:PI Positive value range. MS MS:1002306 value greater than zero Positive value range. PSI:PI Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion. MS MS:1002307 fragmentation ion type Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion. PSI:PI A detector using a fluorescent signal after excitation with light. MS MS:1002308 fluorescence detector A detector using a fluorescent signal after excitation with light. PSI:MS The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM. MS MS:1002309 Byonic: Peptide AbsLogProb The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM. PSI:PI The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein. MS MS:1002310 Byonic: Protein AbsLogProb The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein. PSI:PI The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information. MS MS:1002311 Byonic: Peptide AbsLogProb2D The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information. PSI:PI Compression using MS-Numpress linear prediction compression. MS MS:1002312 MS-Numpress linear prediction compression Compression using MS-Numpress linear prediction compression. https://github.com/ms-numpress/ms-numpress Compression using MS-Numpress positive integer compression. MS MS:1002313 MS-Numpress positive integer compression Compression using MS-Numpress positive integer compression. https://github.com/ms-numpress/ms-numpress Compression using MS-Numpress short logged float compression. MS MS:1002314 MS-Numpress short logged float compression Compression using MS-Numpress short logged float compression. https://github.com/ms-numpress/ms-numpress Indicates a consensus result from several search engine runs. MS MS:1002315 consensus result Indicates a consensus result from several search engine runs. PSI:PI Strict confidence probability score. MS MS:1002316 ProteomeDiscoverer:Amanda:high confidence threshold Strict confidence probability score. PSI:PI Relaxed confidence probability score. MS MS:1002317 ProteomeDiscoverer:Amanda:middle confidence threshold Relaxed confidence probability score. PSI:PI Flag indicating automatic estimation of the workload level. MS MS:1002318 ProteomeDiscoverer:automatic workload Flag indicating automatic estimation of the workload level. PSI:PI The Amanda score of the scoring function for a PSM. MS MS:1002319 Amanda:AmandaScore The Amanda score of the scoring function for a PSM. PSI:PI Maximum dynamic modifications per PSM. MS MS:1002320 ProteomeDiscoverer:max differential modifications Maximum dynamic modifications per PSM. PSI:PI Maximum equal modifications per PSM. MS MS:1002321 ProteomeDiscoverer:max equal modifications Maximum equal modifications per PSM. PSI:PI Minimum peptide length. MS MS:1002322 ProteomeDiscoverer:min peptide length Minimum peptide length. PSI:PI Maximum peptide length. MS MS:1002323 ProteomeDiscoverer:max peptide length Maximum peptide length. PSI:PI Maximum number of same neutral losses. MS MS:1002324 ProteomeDiscoverer:max number neutral loss Maximum number of same neutral losses. PSI:PI Max number of same neutral losses of modifications. MS MS:1002325 ProteomeDiscoverer:max number neutral loss modifications Max number of same neutral losses of modifications. PSI:PI Flag for usage of flanking ions. MS MS:1002326 ProteomeDiscoverer:use flanking ions Flag for usage of flanking ions. PSI:PI The maximum number of possible equal modifications per PSM. MS MS:1002327 ProteomeDiscoverer:max number of same modifs The maximum number of possible equal modifications per PSM. PSI:PI Defines whether a simple deisotoping shall be performed. MS MS:1002328 ProteomeDiscoverer:perform deisotoping Defines whether a simple deisotoping shall be performed. PSI:PI Specifies the fragment ions and neutral losses that are calculated. MS MS:1002329 ProteomeDiscoverer:ion settings Specifies the fragment ions and neutral losses that are calculated. PSI:PI OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter. MS MS:1002330 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. ProteomeDiscoverer:3. Static Modification true OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter. PSI:PI OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter. MS MS:1002331 This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. ProteomeDiscoverer:5. Dynamic Modification true OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter. PSI:PI The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group. MS MS:1002332 lab head The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group. PSI:PI Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process. MS MS:1002333 conversion software Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process. PSI:PI Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML. MS MS:1002334 ProCon Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML. PSI:PI http://www.medizinisches-proteom-center.de/procon Java software designed to convert one of several proteomics identification results formats into PRIDE XML. MS MS:1002335 PRIDE Converter2 Java software designed to convert one of several proteomics identification results formats into PRIDE XML. PMID:22949509 Amanda scoring system for PSM identification. MS MS:1002336 Amanda Amanda scoring system for PSM identification. PSI:PI Andromeda is a peptide search engine. MS MS:1002337 Andromeda Andromeda is a peptide search engine. PSI:PI The probability based score of the Andromeda search engine. MS MS:1002338 Andromeda:score The probability based score of the Andromeda search engine. PSI:PI Estimation of global false discovery rate of peptides with a post-translational modification. MS MS:1002339 site:global FDR Estimation of global false discovery rate of peptides with a post-translational modification. PSI:PI Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project. MS MS:1002340 ProteomeXchange project tag Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project. PSI:PI A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search. MS MS:1002341 second-pass peptide identification A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search. PSI:PI A framework for differential analysis of mass spectrometry data. MZmine MS MS:1002342 mzmine A framework for differential analysis of mass spectrometry data. PMID:16403790 PMID:20650010 OBSOLETE Stability type of the ion. MS MS:1002343 This child of the former purgatory term ion was made obsolete. ion stability type true OBSOLETE Stability type of the ion. PSI:PI Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers. MS MS:1002344 Maltcms Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers. PSI:PI http://maltcms.sf.net Attribute of a single peptide-spectrum match. MS MS:1002345 PSM-level attribute Attribute of a single peptide-spectrum match. PSI:PI Protein group level information. MS MS:1002346 protein group-level identification attribute Protein group level information. PSI:PI Identification confidence metric for a peptide spectrum match. MS MS:1002347 PSM-level identification statistic Identification confidence metric for a peptide spectrum match. PSI:PI Identification confidence metric for a protein group. MS MS:1002348 protein group-level identification statistic Identification confidence metric for a protein group. PSI:PI Positive value range less than or equal to 1. MS MS:1002349 value greater than zero but less than or equal to one Positive value range less than or equal to 1. PSI:PI Estimation of the global false discovery rate of peptide spectrum matches. MS MS:1002350 PSM-level global FDR Estimation of the global false discovery rate of peptide spectrum matches. PSI:PI Estimation of the local false discovery rate of peptide spectrum matches. MS MS:1002351 PSM-level local FDR Estimation of the local false discovery rate of peptide spectrum matches. PSI:PI Estimation of the p-value for peptide spectrum matches. MS MS:1002352 PSM-level p-value Estimation of the p-value for peptide spectrum matches. PSI:PI Estimation of the e-value for peptide spectrum matches. MS MS:1002353 PSM-level e-value Estimation of the e-value for peptide spectrum matches. PSI:PI Estimation of the q-value for peptide spectrum matches. MS MS:1002354 PSM-level q-value Estimation of the q-value for peptide spectrum matches. PSI:PI mzidLibrary FDRScore for peptide spectrum matches. MS MS:1002355 PSM-level FDRScore mzidLibrary FDRScore for peptide spectrum matches. PSI:PI mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. MS MS:1002356 PSM-level combined FDRScore mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. PSI:PI Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum. MS MS:1002357 PSM-level probability Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum. PSI:PI Search engine specific distinct peptide score. MS MS:1002358 search engine specific peptide sequence-level identification statistic Search engine specific distinct peptide score. PSI:PI Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). MS MS:1002359 peptide sequence-level local FDR Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). PSI:PI MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). MS MS:1002360 distinct peptide-level FDRScore MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). PSI:PI Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools. MS MS:1002361 distinct peptide-level combined FDRScore Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools. PSI:PI Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs. MS MS:1002362 peptide sequence-level probability Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs. PSI:PI Search engine specific protein scores. MS MS:1002363 search engine specific score for proteins Search engine specific protein scores. PSI:PI Estimation of the local false discovery rate of proteins. MS MS:1002364 protein-level local FDR Estimation of the local false discovery rate of proteins. PSI:PI MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. MS MS:1002365 FDRScore for proteins MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. PSI:PI MzidLibrary Combined FDRScore for proteins. MS MS:1002366 combined FDRScore for proteins MzidLibrary Combined FDRScore for proteins. PSI:PI Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. MS MS:1002367 probability for proteins Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. PSI:PI Search engine specific protein group scores. MS MS:1002368 search engine specific score for protein groups Search engine specific protein group scores. PSI:PI Estimation of the global false discovery rate of protein groups. MS MS:1002369 protein group-level global FDR Estimation of the global false discovery rate of protein groups. PSI:PI Estimation of the local false discovery rate of protein groups. MS MS:1002370 protein group-level local FDR Estimation of the local false discovery rate of protein groups. PSI:PI Estimation of the p-value for protein groups. MS MS:1002371 protein group-level p-value Estimation of the p-value for protein groups. PSI:PI Estimation of the e-value for protein groups. MS MS:1002372 protein group-level e-value Estimation of the e-value for protein groups. PSI:PI Estimation of the q-value for protein groups. MS MS:1002373 protein group-level q-value Estimation of the q-value for protein groups. PSI:PI mzidLibrary FDRScore for protein groups. MS MS:1002374 protein group-level FDRScore mzidLibrary FDRScore for protein groups. PSI:PI mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. MS MS:1002375 protein group-level combined FDRScore mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. PMID:19253293 Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. MS MS:1002376 protein group-level probability Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. PSI:PI Specifies the threshold value for relaxed scoring. MS MS:1002377 ProteomeDiscoverer:Relaxed Score Threshold Specifies the threshold value for relaxed scoring. PSI:PI Specifies the threshold value for strict scoring. MS MS:1002378 ProteomeDiscoverer:Strict Score Threshold Specifies the threshold value for strict scoring. PSI:PI Cut off score for storing peptides that do not belong to a protein. MS MS:1002379 ProteomeDiscoverer:Peptide Without Protein Cut Off Score Cut off score for storing peptides that do not belong to a protein. PSI:PI Estimation of the false localization rate for modification site assignment. MS MS:1002380 false localization rate Estimation of the false localization rate for modification site assignment. PSI:PI Software for automated LC-MALDI analysis and reporting. MS MS:1002381 MALDI Solutions LC-MALDI Software for automated LC-MALDI analysis and reporting. PSI:PI Shimadzu MALDI-7090: MALDI-TOF-TOF. MS MS:1002382 Shimadzu MALDI-7090 Shimadzu MALDI-7090: MALDI-TOF-TOF. PSI:PI SCiLS software for data acquisition and analysis. MS MS:1002383 SCiLS software SCiLS software for data acquisition and analysis. PSI:MS SCiLS Lab software. MS MS:1002384 SCiLS Lab SCiLS Lab software. PSI:MS SCiLS Lab file format. MS MS:1002385 SCiLS Lab format SCiLS Lab file format. PSI:MS Preprocessing software. MS MS:1002386 preprocessing software Preprocessing software. PSI:PI PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis. MS MS:1002387 PIA PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis. PSI:PI http://www.medizinisches-proteom-center.de/pia A compilation of search engine results in the PIA XML format. MS MS:1002388 PIA XML format A compilation of search engine results in the PIA XML format. PSI:PI A parameter set for a single PIA analysis. MS MS:1002389 PIA workflow parameter A parameter set for a single PIA analysis. PSI:PI Indicates whether the FDR score was calculated for the input file. MS MS:1002390 PIA:FDRScore calculated Indicates whether the FDR score was calculated for the input file. PSI:PI Indicates whether the combined FDR score was calculated for the PIA compilation. MS MS:1002391 PIA:Combined FDRScore calculated Indicates whether the combined FDR score was calculated for the PIA compilation. PSI:PI Indicates whether PSM sets were created. MS MS:1002392 PIA:PSM sets created Indicates whether PSM sets were created. PSI:PI The number of top identifications per spectrum used for the FDR calculation, 0 means all. MS MS:1002393 PIA:used top identifications for FDR The number of top identifications per spectrum used for the FDR calculation, 0 means all. PSI:PI The score given to a protein by any protein inference. MS MS:1002394 PIA:protein score The score given to a protein by any protein inference. PSI:PI The used algorithm for the protein inference using PIA. MS MS:1002395 PIA:protein inference The used algorithm for the protein inference using PIA. PSI:PI A filter used by PIA for the protein inference. MS MS:1002396 PIA:protein inference filter A filter used by PIA for the protein inference. PSI:PI The used scoring method for the protein inference using PIA. MS MS:1002397 PIA:protein inference scoring The used scoring method for the protein inference using PIA. PSI:PI The used base score for the protein inference using PIA. MS MS:1002398 PIA:protein inference used score The used base score for the protein inference using PIA. PSI:PI The method to determine the PSMs used for scoring by the protein inference. MS MS:1002399 PIA:protein inference used PSMs The method to determine the PSMs used for scoring by the protein inference. PSI:PI A filter used for the report generation. MS MS:1002400 PIA:filter A filter used for the report generation. PSI:PI At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members. MS MS:1002401 leading protein At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members. PSI:PI Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence. MS MS:1002402 non-leading protein Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence. PSI:PI An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative. MS MS:1002403 group representative An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative. PSI:PI The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file. MS MS:1002404 count of identified proteins The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file. PSI:PI Details describing a protein cluster. MS MS:1002405 protein group-level result list attribute Details describing a protein cluster. PSI:PI The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. MS MS:1002406 count of identified clusters The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. DOI:10.1002/pmic.201400080 PMID:25092112 An identifier applied to protein groups to indicate that they are linked by shared peptides. MS MS:1002407 cluster identifier An identifier applied to protein groups to indicate that they are linked by shared peptides. PSI:PI The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. MS MS:1002408 number of distinct protein sequences The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. PSI:PI Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group. MS MS:1002409 marginally distinguished protein Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group. PSI:PI Anubis software for selected reaction monitoring data. MS MS:1002410 Anubis Anubis software for selected reaction monitoring data. PSI:PI http://quantitativeproteomics.org/anubis The TraML format for transitions in SRM from the PSI. File extension '.TraML'. MS MS:1002411 TraML format The TraML format for transitions in SRM from the PSI. File extension '.TraML'. PSI:PI http://www.psidev.info/traml Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM). MS MS:1002412 total XIC area Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM). PSI:PI The background area for the quantified transition. MS MS:1002413 product background The background area for the quantified transition. PSI:PI Postprocessing software. MS MS:1002414 postprocessing software Postprocessing software. PSI:PI A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file. MS MS:1002415 protein group passes threshold A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file. PSI:PI Thermo Scientific Orbitrap Fusion. MS MS:1002416 Orbitrap Fusion Thermo Scientific Orbitrap Fusion. PSI:PI Thermo Scientific Orbitrap Fusion with ETD. MS MS:1002417 Orbitrap Fusion ETD Thermo Scientific Orbitrap Fusion with ETD. PSI:PI Thermo Scientific TSQ Quantiva MS. MS MS:1002418 TSQ Quantiva Thermo Scientific TSQ Quantiva MS. PSI:PI Thermo Scientific TSQ Endura MS. MS MS:1002419 TSQ Endura Thermo Scientific TSQ Endura MS. PSI:PI URI that allows access to a PASSEL experiment. MS MS:1002420 PASSEL experiment URI URI that allows access to a PASSEL experiment. PSI:PI Search engine input parameters specific to Paragon. MS MS:1002421 Paragon input parameter Search engine input parameters specific to Paragon. PSI:PI The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation. MS MS:1002422 Paragon: sample type The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation. PSI:PI The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation. MS MS:1002423 Paragon: cysteine alkylation The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation. PSI:PI The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument. MS MS:1002424 Paragon: instrument setting The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument. PSI:PI The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search. MS MS:1002425 Paragon: search effort The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search. PSI:PI A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions. MS MS:1002426 Paragon: ID focus A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions. PSI:PI The Paragon method setting that controls whether FDR analysis is conducted. MS MS:1002427 Paragon: FDR analysis The Paragon method setting that controls whether FDR analysis is conducted. PSI:PI The Paragon method setting that controls whether quantitation analysis is conducted. MS MS:1002428 Paragon: quantitation The Paragon method setting that controls whether quantitation analysis is conducted. PSI:PI The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples. MS MS:1002429 Paragon: background correction The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples. PSI:PI The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity. MS MS:1002430 Paragon: bias correction The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity. PSI:PI The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios. MS MS:1002431 Paragon: channel to use as denominator in ratios The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios. PSI:PI Search engine specific metadata that are not user-controlled settings. MS MS:1002432 search engine specific input metadata Search engine specific metadata that are not user-controlled settings. PSI:PI This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result. MS MS:1002433 Paragon: modified data dictionary or parameter translation This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result. PSI:PI Number of spectra in a search. MS MS:1002434 number of spectra searched Number of spectra in a search. PSI:PI The time that a data processing action was started. MS MS:1002435 data processing start time The time that a data processing action was started. PSI:MS The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done. MS MS:1002436 Paragon: digestion The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done. PSI:PI The number of decoy sequences, if the concatenated target-decoy approach is used. MS MS:1002437 number of decoy sequences The number of decoy sequences, if the concatenated target-decoy approach is used. PSI:PI Information about the list of PSMs (SpectrumIdentificationList). MS MS:1002438 spectrum identification list result details Information about the list of PSMs (SpectrumIdentificationList). PSI:PI A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult. MS MS:1002439 final PSM list A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult. PSI:PI A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult. MS MS:1002440 intermediate PSM list A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult. PSI:PI AIA Analytical Data Interchange file format for mass spectrometry data. MS MS:1002441 Andi-MS format AIA Analytical Data Interchange file format for mass spectrometry data. PSI:PI The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. MS MS:1002442 chromatograph file format The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. PSI:PI AIA Analytical Data Interchange file format for chromatography data. MS MS:1002443 Andi-CHROM format AIA Analytical Data Interchange file format for chromatography data. PSI:PI The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1002444 6420 Triple Quadrupole LC/MS The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity. MS MS:1002445 6460 Triple Quadrupole LC/MS The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity. PSI:MS The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity. MS MS:1002446 6490 Triple Quadrupole LC/MS The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity. PSI:MS The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects. MS MS:1002447 Paragon:special factor The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects. PSI:PI The PEAKS inChorus peptide score. MS MS:1002448 PEAKS:inChorusPeptideScore The PEAKS inChorus peptide score. PSI:PI The PEAKS inChorus protein score. MS MS:1002449 PEAKS:inChorusProteinScore The PEAKS inChorus protein score. PSI:PI Ion b-H3PO4: b ion with lost phosphoric acid. MS MS:1002450 param: b ion-H3PO4 DEPRECATED Ion b-H3PO4: b ion with lost phosphoric acid. PSI:PI Ion y-H3PO4: y ion with lost phosphoric acid. MS MS:1002451 param: y ion-H3PO4 DEPRECATED Ion y-H3PO4: y ion with lost phosphoric acid. PSI:PI The Maltcms Graphical User Interface. MS MS:1002452 Maui The Maltcms Graphical User Interface. PSI:PI http://maltcms.sf.net No fixed modifications are included as a parameter for the search, and therefore they are not reported. MS MS:1002453 No fixed modifications searched No fixed modifications are included as a parameter for the search, and therefore they are not reported. PSI:PI No variable modifications are included as a parameter for the search, and therefore they are not reported. MS MS:1002454 No variable modifications searched No variable modifications are included as a parameter for the search, and therefore they are not reported. PSI:PI OBSOLETE Neutral loss of water. MS MS:1002455 This term was obsoleted because it should be replaced by MS:1000336 with value H2O. H2O neutral loss true OBSOLETE Neutral loss of water. PSI:PI OBSOLETE Neutral loss of ammonia. MS MS:1002456 This term was obsoleted because it should be replaced by MS:1000336 with value NH3. NH3 neutral loss true OBSOLETE Neutral loss of ammonia. PSI:PI OBSOLETE Neutral loss of phosphoric acid. MS MS:1002457 This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4. H3PO4 neutral loss true OBSOLETE Neutral loss of phosphoric acid. PSI:PI PeptideShaker is a software for the interpretation of proteomics identification results. MS MS:1002458 PeptideShaker PeptideShaker is a software for the interpretation of proteomics identification results. PSI:PI http://peptide-shaker.googlecode.com MS Amanda csv output format. MS MS:1002459 MS Amanda csv format MS Amanda csv output format. PSI:PI Estimation of the global false negative rate of protein groups. MS MS:1002460 protein group-level global FNR Estimation of the global false negative rate of protein groups. PSI:PI Estimation of the global confidence of protein groups. MS MS:1002461 protein group-level confidence Estimation of the global confidence of protein groups. PSI:PI Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). MS MS:1002462 peptide sequence-level global FNR Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). PSI:PI Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). MS MS:1002463 peptide sequence-level global confidence Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). PSI:PI Estimation of the global false negative rate of peptide spectrum matches. MS MS:1002464 PSM-level global FNR Estimation of the global false negative rate of peptide spectrum matches. PSI:PI Estimation of the global confidence of peptide spectrum matches. MS MS:1002465 PSM-level global confidence Estimation of the global confidence of peptide spectrum matches. PSI:PI The probability based PeptideShaker PSM score. MS MS:1002466 PeptideShaker PSM score The probability based PeptideShaker PSM score. PSI:PI The probability based PeptideShaker PSM confidence. MS MS:1002467 PeptideShaker PSM confidence The probability based PeptideShaker PSM confidence. PSI:PI The probability based PeptideShaker peptide score. MS MS:1002468 PeptideShaker peptide score The probability based PeptideShaker peptide score. PSI:PI The probability based PeptideShaker peptide confidence. MS MS:1002469 PeptideShaker peptide confidence The probability based PeptideShaker peptide confidence. PSI:PI The probability based PeptideShaker protein group score. MS MS:1002470 PeptideShaker protein group score The probability based PeptideShaker protein group score. PSI:PI The probability based PeptideShaker protein group confidence. MS MS:1002471 PeptideShaker protein group confidence The probability based PeptideShaker protein group confidence. PSI:PI A collision-induced dissociation process that occurs in a trap-type collision cell. MS MS:1002472 trap-type collision-induced dissociation A collision-induced dissociation process that occurs in a trap-type collision cell. PSI:PI The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine. MS MS:1002473 ion series considered in search The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine. PSI:PI The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group. MS MS:1002474 ProteoAnnotator:non-canonical gene model score The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group. PSI:PI The count of the number of peptide sequences mapped to non-canonical gene models only within the group. MS MS:1002475 ProteoAnnotator:count alternative peptides The count of the number of peptide sequences mapped to non-canonical gene models only within the group. PSI:PI Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated. MS MS:1002476 ion mobility drift time Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated. PSI:MS Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1002477 mean ion mobility drift time array Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum. binary-data-type:MS:1000521 MS MS:1002478 mean charge array Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum. PSI:MS binary-data-type:MS:1000521 32-bit float Regular expression. MS MS:1002479 regular expression Regular expression. PSI:PI (10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&'<>])[^ \r \v\f])+). MS MS:1002480 regular expression for a digital object identifier (DOI) (10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&'<>])[^ \r \v\f])+). PSI:PI http://dx.doi.org/ A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV. MS MS:1002481 higher energy beam-type collision-induced dissociation A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV. PSI:MS Estimated statistical threshold. MS MS:1002482 statistical threshold Estimated statistical threshold. PSI:MS Estimated statistical threshold at PSM-level. MS MS:1002483 PSM-level statistical threshold Estimated statistical threshold at PSM-level. PSI:MS Estimated statistical threshold at peptide-level. MS MS:1002484 peptide-level statistical threshold Estimated statistical threshold at peptide-level. PSI:MS Estimated statistical threshold at protein-level. MS MS:1002485 protein-level statistical threshold Estimated statistical threshold at protein-level. PSI:MS Estimated statistical threshold at protein group-level. MS MS:1002486 protein group-level statistical threshold Estimated statistical threshold at protein group-level. PSI:PI Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002487 MassIVE dataset identifier Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002488 MassIVE dataset URI URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI Details describing a special processing. MS MS:1002489 special processing Details describing a special processing. PSI:PI Peptide-level scoring performed. MS MS:1002490 peptide-level scoring Peptide-level scoring performed. PSI:PI Modification localization scoring performed. MS MS:1002491 modification localization scoring Modification localization scoring performed. PSI:PI Consensus multiple search engine approach performed. MS MS:1002492 consensus scoring Consensus multiple search engine approach performed. PSI:PI Sample pre-fractionation performed. MS MS:1002493 sample pre-fractionation Sample pre-fractionation performed. PSI:PI Crosslinking search performed. cross-linking search MS MS:1002494 crosslinking search Crosslinking search performed. PSI:PI No special processing performed. MS MS:1002495 no special processing No special processing performed. PSI:PI Group PSMs by distinct peptide sequence ignoring modifications. MS MS:1002496 group PSMs by sequence Group PSMs by distinct peptide sequence ignoring modifications. PSI:PI Group PSMs by distinct peptide sequence with taking modifications into account. MS MS:1002497 group PSMs by sequence with modifications Group PSMs by distinct peptide sequence with taking modifications into account. PSI:PI Group PSMs by distinct peptide sequence with taking modifications and charge into account. MS MS:1002498 group PSMs by sequence with modifications and charge Group PSMs by distinct peptide sequence with taking modifications and charge into account. PSI:PI OBSOLETE Peptide level score. MS MS:1002499 This term was obsoleted because it was never intended to go in the CV. peptide level score true OBSOLETE Peptide level score. PSI:PI A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file. MS MS:1002500 peptide passes threshold A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file. PSI:PI Indicating that no PSM threshold was used. MS MS:1002501 no PSM threshold Indicating that no PSM threshold was used. PSI:PI Indicating that no peptide-level threshold was used. MS MS:1002502 no peptide-level threshold Indicating that no peptide-level threshold was used. PSI:PI Flags a PSM that it is used for peptide-level scoring. MS MS:1002503 PSM is used for peptide-level scoring Flags a PSM that it is used for peptide-level scoring. PSI:PI The order of modifications to be referenced elsewhere in the document. MS MS:1002504 modification index The order of modifications to be referenced elsewhere in the document. PSI:PI (?<MOD_INDEX>[0-9]+):(?<SCORE>[01][.][0-9]+(?:[Ee][+-]?[0-9]+)?):(?<POSITION>[0-9]+(?:[|][0-9]+)*):(?<PASS_THRESHOLD>true|false) MS MS:1002505 regular expression for modification localization scoring (?<MOD_INDEX>[0-9]+):(?<SCORE>[01][.][0-9]+(?:[Ee][+-]?[0-9]+)?):(?<POSITION>[0-9]+(?:[|][0-9]+)*):(?<PASS_THRESHOLD>true|false) PSI:PI Modification position score. MS MS:1002506 modification position score Modification position score. PSI:PI Mod position score: false localization rate. MS MS:1002507 modification rescoring:false localization rate Mod position score: false localization rate. PSI:PI Crosslinking attribute. cross-linking attribute MS MS:1002508 crosslinking attribute Crosslinking attribute. PSI:PI The crosslinking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. cross-link donor MS MS:1002509 crosslink donor The crosslinking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. PSI:PI Crosslinking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. cross-link acceptor MS MS:1002510 crosslink acceptor Crosslinking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. PSI:PI Crosslinked spectrum identification item. cross-link spectrum identification item MS MS:1002511 crosslink spectrum identification item Crosslinked spectrum identification item. PSI:PI Crosslinking scoring value. cross-linking score MS MS:1002512 crosslinking score Crosslinking scoring value. PSI:PI The absolute abundance of protein in a cell. MS MS:1002513 molecules per cell The absolute abundance of protein in a cell. PSI:PI Absolute quantitation analysis. MS MS:1002514 absolute quantitation analysis Absolute quantitation analysis. PSI:PI States whether an internal peptide reference is used or not in absolute quantitation analysis. MS MS:1002515 internal peptide reference used States whether an internal peptide reference is used or not in absolute quantitation analysis. PSI:PI States whether an internal protein reference is used or not in absolute quantitation analysis. MS MS:1002516 internal protein reference used States whether an internal protein reference is used or not in absolute quantitation analysis. PSI:PI The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis. MS MS:1002517 internal reference abundance The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis. PSI:PI The data type normalised abundance for protein groups produced by Progenesis LC-MS. MS MS:1002518 Progenesis:protein group normalised abundance The data type normalised abundance for protein groups produced by Progenesis LC-MS. PSI:PI The data type raw abundance for protein groups produced by Progenesis LC-MS. MS MS:1002519 Progenesis:protein group raw abundance The data type raw abundance for protein groups produced by Progenesis LC-MS. PSI:PI Peptide group identifier for peptide-level stats. MS MS:1002520 peptide group ID Peptide group identifier for peptide-level stats. PSI:PI A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position. MS MS:1002521 mass spectrometry imaging A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position. PSI:PI Determine 1st static terminal post-translational modifications (PTMs). MS MS:1002522 ProteomeDiscoverer:1. Static Terminal Modification Determine 1st static terminal post-translational modifications (PTMs). PSI:PI Thermo Scientific Q Exactive. MS MS:1002523 Q Exactive HF Thermo Scientific Q Exactive. PSI:PI Thermo Scientific PepFinder BioPharma analysis software. MS MS:1002524 PepFinder Thermo Scientific PepFinder BioPharma analysis software. PSI:PI Thermo Scientific TSQ 8000 Evo MS. MS MS:1002525 TSQ 8000 Evo Thermo Scientific TSQ 8000 Evo MS. PSI:PI Thermo Scientific Exactive Plus MS. MS MS:1002526 Exactive Plus Thermo Scientific Exactive Plus MS. PSI:PI Instrument specific scan properties that are associated with a value. MS MS:1002527 instrument specific scan attribute Instrument specific scan properties that are associated with a value. PSI:PI Synchronous prefilter selection. SPS MS MS:1002528 synchronous prefilter selection Synchronous prefilter selection. PSI:PI A data array of resolution values. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1002529 resolution array A data array of resolution values. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of signal baseline values (the signal in the absence of analytes). binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1002530 baseline array A data array of signal baseline values (the signal in the absence of analytes). PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data. MS MS:1002531 UIMF format SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data. PSI:MS Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger. MS MS:1002532 UIMF nativeID format Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger. PSI:MS SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer. MS MS:1002533 TripleTOF 6600 SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer. PSI:MS The ProLuCID result 'XCorr'. MS MS:1002534 ProLuCID:xcorr The ProLuCID result 'XCorr'. PSI:PI The ProLuCID result 'DeltaCn'. MS MS:1002535 ProLuCID:deltacn The ProLuCID result 'DeltaCn'. PSI:PI D-Score for PTM site location at the PSM-level. MS MS:1002536 D-Score D-Score for PTM site location at the PSM-level. PMID:23307401 MD-Score for PTM site location at the PSM-level. MS MS:1002537 MD-Score MD-Score for PTM site location at the PSM-level. PMID:21057138 Localization confidence metric for a post translational modification (PTM). MS MS:1002538 PTM localization confidence metric Localization confidence metric for a post translational modification (PTM). PSI:PI PeptideShaker quality criteria for the confidence of PTM localizations. MS MS:1002539 PeptideShaker PTM confidence type PeptideShaker quality criteria for the confidence of PTM localizations. PSI:PI PeptideShaker quality criteria for the confidence of PSM's. MS MS:1002540 PeptideShaker PSM confidence type PeptideShaker quality criteria for the confidence of PSM's. PSI:PI PeptideShaker quality criteria for the confidence of peptide identifications. MS MS:1002541 PeptideShaker peptide confidence type PeptideShaker quality criteria for the confidence of peptide identifications. PSI:PI PeptideShaker quality criteria for the confidence of protein identifications. MS MS:1002542 PeptideShaker protein confidence type PeptideShaker quality criteria for the confidence of protein identifications. PSI:PI Target/Decoy based FDR estimation for crosslinking peptide-identifications. MS MS:1002543 xiFDR Target/Decoy based FDR estimation for crosslinking peptide-identifications. PSI:PI Search engine for crosslinked peptides. MS MS:1002544 xi Search engine for crosslinked peptides. PSI:PI The xi result 'Score'. MS MS:1002545 xi:score The xi result 'Score'. PSI:PI A software package to convert Skyline report to mzQuantML. MS MS:1002546 Skyline mzQuantML converter A software package to convert Skyline report to mzQuantML. PSI:PI http://code.google.com/p/srm-mzquantml-convertor/ A normalized spectral abundance factor (NSAF). MS MS:1002547 normalized spectral abundance factor A normalized spectral abundance factor (NSAF). DOI:10.1021/pr060161n PMID:16944946 A distributed normalized spectral abundance factor (dNSAF). MS MS:1002548 distributed normalized spectral abundance factor A distributed normalized spectral abundance factor (dNSAF). DOI:10.1021/ac9023999 PMID:20166708 Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence. MS MS:1002549 PTM localization distinct peptide-level statistic Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence. PSI:PI phosphoRS score for PTM site location at the peptide-level. MS MS:1002550 peptide:phosphoRS score phosphoRS score for PTM site location at the peptide-level. PSI:PI A-score for PTM site location at the peptide-level. MS MS:1002551 peptide:Ascore A-score for PTM site location at the peptide-level. PSI:PI H-Score for peptide phosphorylation site location at the peptide-level. MS MS:1002552 peptide:H-Score H-Score for peptide phosphorylation site location at the peptide-level. PSI:PI D-Score for PTM site location at the peptide-level. MS MS:1002553 peptide:D-Score D-Score for PTM site location at the peptide-level. PSI:PI MD-Score for PTM site location at the peptide-level. MS MS:1002554 peptide:MD-Score MD-Score for PTM site location at the peptide-level. PSI:PI Threshold for PTM site location score. MS MS:1002555 PTM localization score threshold Threshold for PTM site location score. PSI:PI Threshold for Ascore PTM site location score. MS MS:1002556 Ascore threshold Threshold for Ascore PTM site location score. PSI:PI Threshold for D-score PTM site location score. MS MS:1002557 D-Score threshold Threshold for D-score PTM site location score. PSI:PI Threshold for MD-score PTM site location score. MS MS:1002558 MD-Score threshold Threshold for MD-score PTM site location score. PSI:PI Threshold for H-score PTM site location score. MS MS:1002559 H-Score threshold Threshold for H-score PTM site location score. PSI:PI Threshold for DeBunker PTM site location score. MS MS:1002560 DeBunker:score threshold Threshold for DeBunker PTM site location score. PSI:PI Threshold for Mascot PTM site assignment confidence. MS MS:1002561 Mascot:PTM site assignment confidence threshold Threshold for Mascot PTM site assignment confidence. PSI:PI Threshold for MSQuant:PTM-score. MS MS:1002562 MSQuant:PTM-score threshold Threshold for MSQuant:PTM-score. PSI:PI Threshold for MaxQuant:PTM Score. MS MS:1002563 MaxQuant:PTM Score threshold Threshold for MaxQuant:PTM Score. PSI:PI Threshold for MaxQuant:P-site localization probability. MS MS:1002564 MaxQuant:P-site localization probability threshold Threshold for MaxQuant:P-site localization probability. PSI:PI Threshold for MaxQuant:PTM Delta Score. MS MS:1002565 MaxQuant:PTM Delta Score threshold Threshold for MaxQuant:PTM Delta Score. PSI:PI Threshold for MaxQuant:Phospho (STY) Probabilities. MS MS:1002566 MaxQuant:Phospho (STY) Probabilities threshold Threshold for MaxQuant:Phospho (STY) Probabilities. PSI:PI Threshold for phosphoRS score. MS MS:1002567 phosphoRS score threshold Threshold for phosphoRS score. PSI:PI Threshold for phosphoRS site probability. MS MS:1002568 phosphoRS site probability threshold Threshold for phosphoRS site probability. PSI:PI Number of spectra processed at once in a ProteomeDiscoverer search. MS MS:1002569 ProteomeDiscoverer:Number of Spectra Processed At Once Number of spectra processed at once in a ProteomeDiscoverer search. PSI:PI A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group. MS MS:1002570 sequence multiply subsumable protein A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group. PSI:PI A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group. MS MS:1002571 spectrum multiply subsumable protein A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group. PSI:PI Estimated statistical threshold used for protein detection. MS MS:1002572 protein detection statistical threshold Estimated statistical threshold used for protein detection. PSI:MS Estimated statistical threshold used for spectrum identification. MS MS:1002573 spectrum identification statistical threshold Estimated statistical threshold used for spectrum identification. PSI:MS A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. MS MS:1002574 ASAPRatio A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. PSI:PI Tide open-source sequence search program developed at the University of Washington. MS MS:1002575 Tide Tide open-source sequence search program developed at the University of Washington. PMID:21761931 Andromeda result file output format. MS MS:1002576 Andromeda result format Andromeda result file output format. PSI:PI SCIEX 2000 QTRAP. MS MS:1002577 2000 QTRAP SCIEX 2000 QTRAP. PSI:MS SCIEX 2500 QTRAP. MS MS:1002578 2500 QTRAP SCIEX 2500 QTRAP. PSI:MS SCIEX 3500 QTRAP. MS MS:1002579 3500 QTRAP SCIEX 3500 QTRAP. PSI:MS SCIEX QTRAP 4500. MS MS:1002580 QTRAP 4500 SCIEX QTRAP 4500. PSI:MS SCIEX QTRAP 6500. MS MS:1002581 QTRAP 6500 SCIEX QTRAP 6500. PSI:MS SCIEX QTRAP 6500+. MS MS:1002582 QTRAP 6500+ SCIEX QTRAP 6500+. PSI:MS SCIEX TripleTOF 4600 time-of-flight mass spectrometer. MS MS:1002583 TripleTOF 4600 SCIEX TripleTOF 4600 time-of-flight mass spectrometer. PSI:MS SCIEX TripleTOF 5600+ time-of-flight mass spectrometer. MS MS:1002584 TripleTOF 5600+ SCIEX TripleTOF 5600+ time-of-flight mass spectrometer. PSI:MS Applied Biosystems/MDS SCIEX API 100 MS. MS MS:1002585 API 100 Applied Biosystems/MDS SCIEX API 100 MS. PSI:MS Applied Biosystems/MDS SCIEX API 100LC MS. MS MS:1002586 API 100LC Applied Biosystems/MDS SCIEX API 100LC MS. PSI:MS Applied Biosystems/MDS SCIEX API 165 MS. MS MS:1002587 API 165 Applied Biosystems/MDS SCIEX API 165 MS. PSI:MS Applied Biosystems/MDS SCIEX API 300 MS. MS MS:1002588 API 300 Applied Biosystems/MDS SCIEX API 300 MS. PSI:MS Applied Biosystems/MDS SCIEX API 350 MS. MS MS:1002589 API 350 Applied Biosystems/MDS SCIEX API 350 MS. PSI:MS Applied Biosystems/MDS SCIEX API 365 MS. MS MS:1002590 API 365 Applied Biosystems/MDS SCIEX API 365 MS. PSI:MS SCIEX Triple Quad 3500. MS MS:1002591 Triple Quad 3500 SCIEX Triple Quad 3500. PSI:MS SCIEX Triple Quad 4500. MS MS:1002592 Triple Quad 4500 SCIEX Triple Quad 4500. PSI:MS SCIEX Triple Quad 5500. MS MS:1002593 Triple Quad 5500 SCIEX Triple Quad 5500. PSI:MS SCIEX Triple Quad 6500. MS MS:1002594 Triple Quad 6500 SCIEX Triple Quad 6500. PSI:MS SCIEX Triple Quad 6500+. MS MS:1002595 Triple Quad 6500+ SCIEX Triple Quad 6500+. PSI:MS The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute. MS MS:1002596 ProLuCID The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute. PMID:26171723 MS1 file format for MS1 spectral data. MS MS:1002597 MS1 format MS1 file format for MS1 spectral data. DOI:10.1002/rcm.1603 PMID:15317041 Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches. MS MS:1002598 DTASelect Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches. PMID:12643522 http://fields.scripps.edu/DTASelect/ Spectral Hash key, an unique identifier for spectra. MS MS:1002599 splash key Spectral Hash key, an unique identifier for spectra. PMID:27824832 Internal data and submission format of the PRIDE database. MS MS:1002600 PRIDE XML Internal data and submission format of the PRIDE database. http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd Tabular result format for proteomics and metabolomics experiments. MS MS:1002601 mzTab Tabular result format for proteomics and metabolomics experiments. PMID:24980485 http://www.psidev.info/mztab/ Reagent used in labeled quantification methods. MS MS:1002602 sample label Reagent used in labeled quantification methods. PSI:PI Isotope coded affinity tag reagent. MS MS:1002603 ICAT reagent Isotope coded affinity tag reagent. PSI:PI The name of the sample labelled with the heavy ICAT label. MS MS:1002604 ICAT heavy reagent The name of the sample labelled with the heavy ICAT label. PSI:PI The name of the sample labelled with the light ICAT label. MS MS:1002605 ICAT light reagent The name of the sample labelled with the light ICAT label. PSI:PI Isotope coded protein labeling reagent. MS MS:1002606 ICPL reagent Isotope coded protein labeling reagent. PSI:PI The name of the sample labelled with the ICPL reagent 0. MS MS:1002607 ICPL reagent 0 The name of the sample labelled with the ICPL reagent 0. PSI:PI The name of the sample labelled with the ICPL reagent 4. MS MS:1002608 ICPL reagent 4 The name of the sample labelled with the ICPL reagent 4. PSI:PI The name of the sample labelled with the ICPL reagent 6. MS MS:1002609 ICPL reagent 6 The name of the sample labelled with the ICPL reagent 6. PSI:PI The name of the sample labelled with the ICPL reagent 10. MS MS:1002610 ICPL reagent 10 The name of the sample labelled with the ICPL reagent 10. PSI:PI Stable isotope labeling with amino acids in cell culture reagent. MS MS:1002611 SILAC reagent Stable isotope labeling with amino acids in cell culture reagent. PSI:PI The name of the sample labelled with the heavy SILAC label. MS MS:1002612 SILAC heavy reagent The name of the sample labelled with the heavy SILAC label. PSI:PI The name of the sample labelled with the medium SILAC label. MS MS:1002613 SILAC medium reagent The name of the sample labelled with the medium SILAC label. PSI:PI The name of the sample labelled with the light SILAC label. MS MS:1002614 SILAC light reagent The name of the sample labelled with the light SILAC label. PSI:PI Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling. MS MS:1002615 TMT reagent Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling. PSI:PI The name of the sample labelled with the TMT reagent 126. MS MS:1002616 TMT reagent 126 The name of the sample labelled with the TMT reagent 126. PSI:PI The name of the sample labelled with the TMT reagent 127. MS MS:1002617 TMT reagent 127 The name of the sample labelled with the TMT reagent 127. PSI:PI The name of the sample labelled with the TMT reagent 128. MS MS:1002618 TMT reagent 128 The name of the sample labelled with the TMT reagent 128. PSI:PI The name of the sample labelled with the TMT reagent 129. MS MS:1002619 TMT reagent 129 The name of the sample labelled with the TMT reagent 129. PSI:PI The name of the sample labelled with the TMT reagent 130. MS MS:1002620 TMT reagent 130 The name of the sample labelled with the TMT reagent 130. PSI:PI The name of the sample labelled with the TMT reagent 131. MS MS:1002621 TMT reagent 131 The name of the sample labelled with the TMT reagent 131. PSI:PI Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent. MS MS:1002622 iTRAQ reagent Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent. PSI:PI The name of the sample labelled with the iTRAQ reagent 113. MS MS:1002623 iTRAQ reagent 113 The name of the sample labelled with the iTRAQ reagent 113. PSI:PI The name of the sample labelled with the iTRAQ reagent 114. MS MS:1002624 iTRAQ reagent 114 The name of the sample labelled with the iTRAQ reagent 114. PSI:PI The name of the sample labelled with the iTRAQ reagent 115. MS MS:1002625 iTRAQ reagent 115 The name of the sample labelled with the iTRAQ reagent 115. PSI:PI The name of the sample labelled with the iTRAQ reagent 116. MS MS:1002626 iTRAQ reagent 116 The name of the sample labelled with the iTRAQ reagent 116. PSI:PI The name of the sample labelled with the iTRAQ reagent 117. MS MS:1002627 iTRAQ reagent 117 The name of the sample labelled with the iTRAQ reagent 117. PSI:PI The name of the sample labelled with the iTRAQ reagent 118. MS MS:1002628 iTRAQ reagent 118 The name of the sample labelled with the iTRAQ reagent 118. PSI:PI The name of the sample labelled with the iTRAQ reagent 119. MS MS:1002629 iTRAQ reagent 119 The name of the sample labelled with the iTRAQ reagent 119. PSI:PI The name of the sample labelled with the iTRAQ reagent 121. MS MS:1002630 iTRAQ reagent 121 The name of the sample labelled with the iTRAQ reagent 121. PSI:PI Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy). EThcD MS MS:1002631 electron-transfer/higher-energy collision dissociation Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy). PSI:PI Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002632 jPOST dataset identifier Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002633 jPOST dataset URI URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI Thermo Scientific Q Exactive Plus. MS MS:1002634 Q Exactive Plus Thermo Scientific Q Exactive Plus. PSI:PI Proteogenomics search performed. MS MS:1002635 proteogenomics search Proteogenomics search performed. PSI:PI Proteogenomics attribute. MS MS:1002636 proteogenomics attribute Proteogenomics attribute. PSI:PI The name or number of the chromosome to which a given peptide has been mapped. MS MS:1002637 chromosome name The name or number of the chromosome to which a given peptide has been mapped. PSI:PI The strand (+ or -) to which the peptide has been mapped. MS MS:1002638 chromosome strand The strand (+ or -) to which the peptide has been mapped. PSI:PI OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system. MS MS:1002639 This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. peptide start on chromosome true OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system. PSI:PI The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system. MS MS:1002640 peptide end on chromosome The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system. PSI:PI The number of exons to which the peptide has been mapped. MS MS:1002641 peptide exon count The number of exons to which the peptide has been mapped. PSI:PI A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length. MS MS:1002642 peptide exon nucleotide sizes A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length. PSI:PI A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome. MS MS:1002643 peptide start positions on chromosome A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome. PSI:PI The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference. MS MS:1002644 genome reference version The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference. PSI:PI Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data. MS MS:1002645 MSDK Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data. PSI:PI http://msdk.github.io/ Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated. nativeID format, combined spectra MS MS:1002646 native spectrum identifier format, combined spectra Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated. PSI:PI Thermo comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002647 Thermo nativeID format, combined spectra Thermo comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Waters comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002648 Waters nativeID format, combined spectra Waters comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI WIFF comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002649 WIFF nativeID format, combined spectra WIFF comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002650 Bruker/Agilent YEP nativeID format, combined spectra Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002651 Bruker BAF nativeID format, combined spectra Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002652 The nativeID must be the same as the source file ID. Bruker FID nativeID format, combined spectra Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002653 Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. multiple peak list nativeID format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002654 The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. single peak list nativeID format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002655 Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. scan number only nativeID format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002656 Used for conversion from mzData. The spectrum id attribute is referenced. spectrum identifier nativeID format, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002657 A unique identifier of a spectrum stored in an mzML file. mzML unique identifier, combined spectra Comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Identification parameter for the search engine run. MS MS:1002658 identification parameter Identification parameter for the search engine run. PSI:PI Text-based format used by UniProtKB for sequence entries. MS MS:1002659 UniProtKB text sequence format Text-based format used by UniProtKB for sequence entries. PSI:PI XML-based format used by UniProtKB for sequence entries. MS MS:1002660 UniProtKB XML sequence format XML-based format used by UniProtKB for sequence entries. PSI:PI Morpheus search engine. MS MS:1002661 Morpheus Morpheus search engine. PMID:23323968 Morpheus score for PSMs. MS MS:1002662 Morpheus:Morpheus score Morpheus score for PSMs. PSI:PI Summed Morpheus score for protein groups. MS MS:1002663 Morpheus:summed Morpheus score Summed Morpheus score for protein groups. PSI:PI Parent term for interaction scores derived from crosslinking. interaction score derived from cross-linking MS MS:1002664 interaction score derived from crosslinking Parent term for interaction scores derived from crosslinking. PSI:PI ((?<int_ID>[0-9]+)[.](?<SUFFIX>[a|b]):(?<POS>[0-9]+|null):(?<SCORE_OR_VALUE>[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?):(?<PASS_THRESHOLD>true|false))|(?<SCORE_ONLY>[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?) regular expression for interaction scores derived from cross-linking MS MS:1002665 regular expression for interaction scores derived from crosslinking ((?<int_ID>[0-9]+)[.](?<SUFFIX>[a|b]):(?<POS>[0-9]+|null):(?<SCORE_OR_VALUE>[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?):(?<PASS_THRESHOLD>true|false))|(?<SCORE_ONLY>[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?) PSI:PI Bruker Daltonics' impact II. MS MS:1002666 impact II Bruker Daltonics' impact II. PSI:MS Bruker Daltonics' impact HD. MS MS:1002667 impact HD Bruker Daltonics' impact HD. PSI:MS Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114. MS MS:1002668 frag: iTRAQ 4plex reporter ion Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114. PSI:PI Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113. MS MS:1002669 frag: iTRAQ 8plex reporter ion Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113. PSI:PI Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N. MS MS:1002670 frag: TMT reporter ion Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N. PSI:PI Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C. MS MS:1002671 frag: TMT ETD reporter ion Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C. PSI:PI No statistical threshold for accepting or rejecting that a modification position. MS MS:1002672 no modification threshold No statistical threshold for accepting or rejecting that a modification position. PSI:PI Cross-Linking MS search engine. MS MS:1002673 OpenXQuest Cross-Linking MS search engine. PSI:PI SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer. MS MS:1002674 X500R QTOF SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer. PSI:MS This subsection describes terms which can describe details of crosslinking results. cross-linking result details MS MS:1002675 crosslinking result details This subsection describes terms which can describe details of crosslinking results. PSI:PI Estimation of the global false discovery rate of proteins-pairs in crosslinking experiments. MS MS:1002676 protein-pair-level global FDR Estimation of the global false discovery rate of proteins-pairs in crosslinking experiments. PSI:PI Estimation of the global false discovery rate of residue-pairs in crosslinking experiments. MS MS:1002677 residue-pair-level global FDR Estimation of the global false discovery rate of residue-pairs in crosslinking experiments. PSI:PI A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation. MS MS:1002678 supplemental beam-type collision-induced dissociation A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation. PSI:MS The dissociation of an ion after supplemental collisional excitation. MS MS:1002679 supplemental collision-induced dissociation The dissociation of an ion after supplemental collisional excitation. PSI:MS Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion. MS MS:1002680 supplemental collision energy Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion. PSI:MS OpenXQuest's combined score for a crosslink spectrum match. MS MS:1002681 OpenXQuest:combined score OpenXQuest's combined score for a crosslink spectrum match. PSI:PI OpenXQuest's cross-correlation of crosslinked ions subscore. MS MS:1002682 OpenXQuest:xcorr xlink OpenXQuest's cross-correlation of crosslinked ions subscore. PSI:PI OpenXQuest's cross-correlation of unlinked ions subscore. MS MS:1002683 OpenXQuest:xcorr common OpenXQuest's cross-correlation of unlinked ions subscore. PSI:PI OpenXQuest's match-odds subscore. MS MS:1002684 OpenXQuest:match-odds OpenXQuest's match-odds subscore. PSI:PI OpenXQuest's sum of matched peak intensity subscore. MS MS:1002685 OpenXQuest:intsum OpenXQuest's sum of matched peak intensity subscore. PSI:PI OpenXQuest's weighted percent of total ion current subscore. MS MS:1002686 OpenXQuest:wTIC OpenXQuest's weighted percent of total ion current subscore. PSI:PI Attribute of an item in the result of mass spectrometry proteomics data analysis. MS MS:1002687 analysis attribute Attribute of an item in the result of mass spectrometry proteomics data analysis. PSI:PI Statistic derived from a post-translational modification localization analysis. MS MS:1002688 PTM localization attribute Statistic derived from a post-translational modification localization analysis. PSI:PI Statistic for a single item derived from a post-translational modification localization analysis. MS MS:1002689 PTM localization single result statistic Statistic for a single item derived from a post-translational modification localization analysis. PSI:PI Statistic for all items derived from a post-translational modification localization analysis. MS MS:1002690 PTM localization result list statistic Statistic for all items derived from a post-translational modification localization analysis. PSI:PI Global false localization rate for all localizations in a dataset. MS MS:1002691 global FLR Global false localization rate for all localizations in a dataset. PSI:PI Local false localization rate for the bottom item in list of localizations sorted from most to least confident. MS MS:1002692 local FLR at threshold Local false localization rate for the bottom item in list of localizations sorted from most to least confident. PSI:PI Attribute of an identification item in the result of mass spectrometry proteomics data analysis. MS MS:1002693 identification attribute Attribute of an identification item in the result of mass spectrometry proteomics data analysis. PSI:PI Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis. MS MS:1002694 single identification result attribute Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis. PSI:PI Fragment ion corresponding to an isobaric label artifact. MS MS:1002695 frag: isobaric label ion Fragment ion corresponding to an isobaric label artifact. PSI:PI Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion. MS MS:1002697 secondary isotope peak Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion. PSI:PI An attribute of the protein cluster concept as used in mzIdentML. MS MS:1002698 protein cluster identification attribute An attribute of the protein cluster concept as used in mzIdentML. PSI:PI General property of an entire result list. MS MS:1002699 result list attribute General property of an entire result list. PSI:PI General property of the list of all PSMs. MS MS:1002700 PSM-level result list attribute General property of the list of all PSMs. PSI:PI Statistic pertaining to the full list of all PSMs. MS MS:1002701 PSM-level result list statistic Statistic pertaining to the full list of all PSMs. PSI:PI General property of all peptide sequences in the list. MS MS:1002702 peptide sequence-level result list attribute General property of all peptide sequences in the list. PSI:PI Statistic pertaining to all peptide sequences in the list. MS MS:1002703 peptide sequence-level result list statistic Statistic pertaining to all peptide sequences in the list. PSI:PI Attribute of an entire protein list. MS MS:1002704 protein-level result list attribute Attribute of an entire protein list. PSI:PI A statistical metric of an entire protein list. MS MS:1002705 protein-level result list statistic A statistical metric of an entire protein list. PSI:PI Attrbiute of an entire list of protein groups. MS MS:1002706 protein group-level result list statistic Attrbiute of an entire list of protein groups. PSI:PI Regular expression for LysargiNase. MS MS:1002707 (?=[KR]) Regular expression for LysargiNase. PSI:PI Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues. Tryp-N MS MS:1002708 LysargiNase Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues. PMID:25419962 A data type representing more than a single value. MS MS:1002709 compound data type A data type defining a list of values of a single type. MS MS:1002710 list of type A list of xsd:string. MS MS:1002711 list of strings A list of xsd:integer. MS MS:1002712 list of integers A list of xsd:float. MS MS:1002713 list of floats Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. MS MS:1002714 FLASHDeconv Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. DOI:10.1016/j.cels.2020.01.003 Representation of temperature versus time. MS MS:1002715 temperature chromatogram Representation of temperature versus time. PSI:MS The component or dimension of an object being measured, for example the temperature of an instrument component over time. MS MS:1002716 measured element The component or dimension of an object being measured, for example the temperature of an instrument component over time. PSI:MS Software for processing and exporting Waters MassLynx and waters_connect data. MS MS:1002717 Waters DATA Convert Software for processing and exporting Waters MassLynx and waters_connect data. PSI:MS LECO bench-top GC time-of-flight mass spectrometer. MS MS:1002719 Pegasus BT LECO bench-top GC time-of-flight mass spectrometer. PSI:PI PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra. MS MS:1002720 MSPathFinder PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra. PSI:PI MSPathFinder spectral E-value. MS MS:1002721 MSPathFinder:SpecEValue MSPathFinder spectral E-value. PSI:PI MSPathFinder E-value. MS MS:1002722 MSPathFinder:EValue MSPathFinder E-value. PSI:PI MSPathFinder Q-value. MS MS:1002723 MSPathFinder:QValue MSPathFinder Q-value. PSI:PI MSPathFinder peptide-level Q-value. MS MS:1002724 MSPathFinder:PepQValue MSPathFinder peptide-level Q-value. PSI:PI MSPathFinder raw score. MS MS:1002725 MSPathFinder:RawScore MSPathFinder raw score. PSI:PI Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. MS MS:1002726 SYNAPT G2-Si Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. PSI:PI Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. MS MS:1002727 MALDI SYNAPT G2-Si Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. PSI:PI Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer. MS MS:1002728 Vion IMS QTof Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer. PSI:PI Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer. MS MS:1002729 Xevo G2-XS Tof Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer. PSI:PI Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer. MS MS:1002730 Xevo TQ-XS Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer. PSI:PI Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer. MS MS:1002731 Xevo TQ-S micro Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer. PSI:PI Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. MS MS:1002732 Orbitrap Fusion Lumos Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. PSI:PI The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting. MS MS:1002733 peptide-level spectral count The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting. PSI:PI The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting. MS MS:1002734 peptide ion-level spectral count The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting. PSI:PI The data type of the value reported in a QuantLayer for a feature. MS MS:1002735 feature-level quantification datatype The data type of the value reported in a QuantLayer for a feature. PSI:PI The data type of the value reported in a QuantLayer for a PSM. MS MS:1002736 PSM-level quantification datatype The data type of the value reported in a QuantLayer for a PSM. PSI:PI The data type of the value reported in a QuantLayer for a peptide. MS MS:1002737 peptide-level quantification datatype The data type of the value reported in a QuantLayer for a peptide. PSI:PI The data type of the value reported in a QuantLayer for a protein. MS MS:1002738 protein-level quantification datatype The data type of the value reported in a QuantLayer for a protein. PSI:PI The data type of the value reported in a QuantLayer for a protein group. MS MS:1002739 protein group-level quantification datatype The data type of the value reported in a QuantLayer for a protein group. PSI:PI Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location. MS MS:1002740 unmapped peptide Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location. PSI:PI Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location. MS MS:1002741 unmapped protein Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location. PSI:PI A data array of noise values. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1002742 noise array A data array of noise values. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array). binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1002743 sampled noise m/z array A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array). PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array). binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1002744 sampled noise intensity array A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array). PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array). binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1002745 sampled noise baseline array A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array). PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float Compression using MS-Numpress linear prediction compression and zlib. MS MS:1002746 MS-Numpress linear prediction compression followed by zlib compression Compression using MS-Numpress linear prediction compression and zlib. https://github.com/ms-numpress/ms-numpress Compression using MS-Numpress positive integer compression and zlib. MS MS:1002747 MS-Numpress positive integer compression followed by zlib compression Compression using MS-Numpress positive integer compression and zlib. https://github.com/ms-numpress/ms-numpress Compression using MS-Numpress short logged float compression and zlib. MS MS:1002748 MS-Numpress short logged float compression followed by zlib compression Compression using MS-Numpress short logged float compression and zlib. https://github.com/ms-numpress/ms-numpress Means that Mascot has integrated the search results of database and spectral library search into a single data set. MS MS:1002749 Mascot:IntegratedSpectralLibrarySearch Means that Mascot has integrated the search results of database and spectral library search into a single data set. PSI:PI Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches. MS MS:1002750 NIST MSPepSearch Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches. PSI:PI MSP text format defined by the NIST. MS MS:1002751 NIST MSP format MSP text format defined by the NIST. PSI:PI Database containing spectra. MS MS:1002752 database type spectral library Database containing spectra. PSI:PI Value range for scores. MS MS:1002753 value between 0 and 1000 inclusive Value range for scores. PSI:PI MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum. MS MS:1002754 MSPepSearch:score MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum. PSI:PI A combined MS2 (with fragment ions) and spectral library search. MS MS:1002755 combined ms-ms + spectral library search A combined MS2 (with fragment ions) and spectral library search. PSI:PI Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow. MS MS:1002756 iodoTMT quantitation analysis Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow. PMID:24926564 PSI:PI Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow. MS MS:1002757 glyco-TMT quantitation analysis Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow. PMID:22455665 PSI:PI Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow. MS MS:1002758 aminoxyTMT quantitation analysis Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow. PMID:25337643 PSI:PI Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow. MS MS:1002759 hydrazideTMT quantitation analysis Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow. PMID:25337643 PSI:PI Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow. MS MS:1002760 iTRAQH quantitation analysis Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow. PMID:22926130 PSI:PI Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow. MS MS:1002761 DiART quantitation analysis Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow. PMID:20715779 PSI:PI Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow. MS MS:1002762 DiLeu quantitation analysis Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow. PMID:20715779 PSI:PI The name of the sample labelled with the TMT reagent 127N. MS MS:1002763 TMT reagent 127N The name of the sample labelled with the TMT reagent 127N. PSI:PI The name of the sample labelled with the TMT reagent 127C. MS MS:1002764 TMT reagent 127C The name of the sample labelled with the TMT reagent 127C. PSI:PI The name of the sample labelled with the TMT reagent 128N. MS MS:1002765 TMT reagent 128N The name of the sample labelled with the TMT reagent 128N. PSI:PI The name of the sample labelled with the TMT reagent 128C. MS MS:1002766 TMT reagent 128C The name of the sample labelled with the TMT reagent 128C. PSI:PI The name of the sample labelled with the TMT reagent 129N. MS MS:1002767 TMT reagent 129N The name of the sample labelled with the TMT reagent 129N. PSI:PI The name of the sample labelled with the TMT reagent 129C. MS MS:1002768 TMT reagent 129C The name of the sample labelled with the TMT reagent 129C. PSI:PI The name of the sample labelled with the TMT reagent 130N. MS MS:1002769 TMT reagent 130N The name of the sample labelled with the TMT reagent 130N. PSI:PI The name of the sample labelled with the TMT reagent 130C. MS MS:1002770 TMT reagent 130C The name of the sample labelled with the TMT reagent 130C. PSI:PI Deuterium isobaric amine reactive tag labeling reagent. MS MS:1002771 DiART reagent Deuterium isobaric amine reactive tag labeling reagent. PSI:PI The name of the sample labelled with the DiART reagent 114. MS MS:1002772 DiART reagent 114 The name of the sample labelled with the DiART reagent 114. PSI:PI The name of the sample labelled with the DiART reagent 115. MS MS:1002773 DiART reagent 115 The name of the sample labelled with the DiART reagent 115. PSI:PI The name of the sample labelled with the DiART reagent 116. MS MS:1002774 DiART reagent 116 The name of the sample labelled with the DiART reagent 116. PSI:PI The name of the sample labelled with the DiART reagent 117. MS MS:1002775 DiART reagent 117 The name of the sample labelled with the DiART reagent 117. PSI:PI The name of the sample labelled with the DiART reagent 118. MS MS:1002776 DiART reagent 118 The name of the sample labelled with the DiART reagent 118. PSI:PI The name of the sample labelled with the DiART reagent 119. MS MS:1002777 DiART reagent 119 The name of the sample labelled with the DiART reagent 119. PSI:PI Dimethyl leucine labeling reagent. MS MS:1002778 DiLeu reagent Dimethyl leucine labeling reagent. PSI:PI The name of the sample labelled with the DiLeu reagent 115. MS MS:1002779 DiLeu reagent 115 The name of the sample labelled with the DiLeu reagent 115. PSI:PI The name of the sample labelled with the DiLeu reagent 116. MS MS:1002780 DiLeu reagent 116 The name of the sample labelled with the DiLeu reagent 116. PSI:PI The name of the sample labelled with the DiLeu reagent 117. MS MS:1002781 DiLeu reagent 117 The name of the sample labelled with the DiLeu reagent 117. PSI:PI The name of the sample labelled with the DiLeu reagent 118. MS MS:1002782 DiLeu reagent 118 The name of the sample labelled with the DiLeu reagent 118. PSI:PI The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002783 6550 iFunnel Q-TOF LC/MS The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002784 6550A iFunnel Q-TOF LC/MS The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002785 6520B Q-TOF LC/MS The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002786 6530A Q-TOF LC/MS The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002787 6530B Q-TOF LC/MS The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002788 6538 Q-TOF LC/MS The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002789 6540 Q-TOF LC/MS The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002790 6542 Q-TOF LC/MS The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002791 6545 Q-TOF LC/MS The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002792 6560 Q-TOF LC/MS The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002793 6570 Q-TOF LC/MS The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. MS MS:1002794 6120B Quadrupole LC/MS The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. PSI:MS The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. MS MS:1002795 6150 Quadrupole LC/MS The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. PSI:MS The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002796 6224 Time-of-Flight LC/MS The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002797 6230A Time-of-Flight LC/MS The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. MS MS:1002798 6230B Time-of-Flight LC/MS The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. PSI:MS The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1002799 6430 Triple Quadrupole LC/MS The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1002800 6495A Triple Quadrupole LC/MS The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1002801 6495B Triple Quadrupole LC/MS The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1002802 7000A Triple Quadrupole GC/MS The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. MS MS:1002803 7000B Triple Quadrupole GC/MS The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. PSI:MS The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. MS MS:1002804 7800 Quadrupole ICP-MS The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. PSI:MS The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. MS MS:1002805 8800 Triple Quadrupole ICP-MS The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. PSI:MS Molecular entity having a net positive or negative electric charge. MS MS:1002806 ion Molecular entity having a net positive or negative electric charge. PSI:MS Adduct ion with positive ionization. MS MS:1002807 positive mode adduct ion Adduct ion with positive ionization. PSI:MS Adduct ion with negative ionization. MS MS:1002808 negative mode adduct ion Adduct ion with negative ionization. PSI:MS Nonphysical characteristic attributed to an adduct ion. MS MS:1002809 adduct ion attribute Nonphysical characteristic attributed to an adduct ion. PSI:MS Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator. MS MS:1002810 adduct ion X m/z Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator. PSI:MS Isotope of the matrix molecule M of an adduct formation. MS MS:1002811 adduct ion isotope Isotope of the matrix molecule M of an adduct formation. PSI:MS ([[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}][:digit:]{0,1}[+-]). MS MS:1002812 Regular expression for adduct ion formula ([[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}][:digit:]{0,1}[+-]). PSI:PI Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression. MS MS:1002813 adduct ion formula Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression. PSI:MS An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]. Vs/cm^2 MS MS:1002814 volt-second per square centimeter An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]. PSI:PI Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated. MS MS:1002815 inverse reduced ion mobility Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated. PSI:MS Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1002816 mean ion mobility array Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Bruker TDF raw file format. MS MS:1002817 Bruker TDF format Bruker TDF raw file format. PSI:MS Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. MS MS:1002818 Bruker TDF nativeID format Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. PSI:MS Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1002819 Bruker TDF nativeID format, combined spectra Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton. M + 1.007276 MS MS:1002820 M+H ion Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton. PSI:MS Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M. M - 1.007276 MS MS:1002821 M-H ion Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M. PSI:MS File format developed by the OpenMS team. MS MS:1002822 OpenMS file format File format developed by the OpenMS team. PMID:27575624 OpenMS intermediate identification format. MS MS:1002823 idXML OpenMS intermediate identification format. PSI:PI OpenMS feature file format. MS MS:1002824 featureXML OpenMS feature file format. PSI:PI OpenMS consensus map format. MS MS:1002825 consensusXML OpenMS consensus map format. PSI:PI MetaMorpheus search engine. MS MS:1002826 MetaMorpheus MetaMorpheus search engine. https://github.com/smith-chem-wisc/MetaMorpheus MetaMorpheus score for PSMs. MS MS:1002827 MetaMorpheus:score MetaMorpheus score for PSMs. PSI:PI MetaMorpheus score for protein groups. MS MS:1002828 MetaMorpheus:protein score MetaMorpheus score for protein groups. PSI:PI Feature intensity produced by XCMS findPeaks() from integrated peak intensity. MS MS:1002829 XCMS:into Feature intensity produced by XCMS findPeaks() from integrated peak intensity. PSI:PI Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity. MS MS:1002830 XCMS:intf Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity. PSI:PI Feature intensity produced by XCMS findPeaks() from maximum peak intensity. MS MS:1002831 XCMS:maxo Feature intensity produced by XCMS findPeaks() from maximum peak intensity. PSI:PI Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate. MS MS:1002832 XCMS:area Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate. PSI:PI Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired. MS MS:1002833 alternating polarity mode Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired. PSI:PI The Delta Score reported by Proteome Discoverer version 2. MS MS:1002834 ProteomeDiscoverer:Delta Score The Delta Score reported by Proteome Discoverer version 2. PSI:PI Thermo Fisher Scientific LTQ Orbitrap Classic. MS MS:1002835 LTQ Orbitrap Classic Thermo Fisher Scientific LTQ Orbitrap Classic. PSI:MS Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002836 iProX dataset identifier Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002837 iProX dataset URI URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI mzMLb file format, mzML encapsulated within HDF5. MS MS:1002838 mzMLb format mzMLb file format, mzML encapsulated within HDF5. PSI:PI https://github.com/biospi/mzmlb Conversion of a file format to Proteomics Standards Initiative mzMLb file format. MS MS:1002839 Conversion to mzMLb Conversion of a file format to Proteomics Standards Initiative mzMLb file format. PSI:PI Data belonging to an external reference. MS MS:1002840 external reference data Data belonging to an external reference. PSI:MS The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray. MS MS:1002841 external HDF5 dataset The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray. PSI:PI The position in the external data where the array begins. MS MS:1002842 external offset The position in the external data where the array begins. PSI:PI Describes how many fields an array contains. MS MS:1002843 external array length Describes how many fields an array contains. PSI:PI Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam. MS MS:1002844 Experiment additional parameter Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam. PSI:PI URI of one external file associated to the PRIDE experiment (maybe through a PX submission). MS MS:1002845 Associated file URI URI of one external file associated to the PRIDE experiment (maybe through a PX submission). PSI:PI URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). MS MS:1002846 Associated raw file URI URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). PSI:PI URI associated to one PX submission in ProteomeCentral. MS MS:1002847 ProteomeCentral dataset URI URI associated to one PX submission in ProteomeCentral. PSI:PI URI of one file labeled as 'Result', associated to one PX submission. MS MS:1002848 Result file URI URI of one file labeled as 'Result', associated to one PX submission. PSI:PI URI of one search engine output file associated to one PX submission. MS MS:1002849 Search engine output file URI URI of one search engine output file associated to one PX submission. PSI:PI URI of one of one search engine output file associated to one PX submission. MS MS:1002850 Peak list file URI URI of one of one search engine output file associated to one PX submission. PSI:PI URI of one file labeled as 'Other', associated to one PX submission. MS MS:1002851 Other type file URI URI of one file labeled as 'Other', associated to one PX submission. PSI:PI FTP location of one entire PX data set. MS MS:1002852 Dataset FTP location FTP location of one entire PX data set. PSI:PI A dataset which does not have an associated published manuscript. MS MS:1002853 Dataset with no associated published manuscript A dataset which does not have an associated published manuscript. PSI:PI Dataset has been peer-reviewed somehow. MS MS:1002854 Peer-reviewed dataset Dataset has been peer-reviewed somehow. PSI:PI Dataset that has not been peer-reviewed by any means. MS MS:1002855 Non peer-reviewed dataset Dataset that has not been peer-reviewed by any means. PSI:PI Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission. MS MS:1002856 Supported dataset by repository Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission. PSI:PI Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission. MS MS:1002857 Unsupported dataset by repository Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission. PSI:PI A dataset which has an associated manuscript pending for publication. MS MS:1002858 Dataset with its publication pending A dataset which has an associated manuscript pending for publication. PSI:PI Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE. MS MS:1002859 Additional associated raw file URI Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE. PSI:PI URI of one gel image file associated to one PX submission. MS MS:1002860 Gel image file URI URI of one gel image file associated to one PX submission. PSI:PI All the raw files included in the original dataset (or group of original datasets) have been reanalysed. MS MS:1002861 Reprocessed complete dataset All the raw files included in the original dataset (or group of original datasets) have been reanalysed. PSI:PI A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed. MS MS:1002862 Reprocessed subset dataset A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed. PSI:PI One dataset is a reanalysis of previously published data. MS MS:1002863 Data derived from previous dataset One dataset is a reanalysis of previously published data. PSI:PI No post-translational-modifications are been included in the identified peptides of one dataset. MS MS:1002864 No PTMs are included in the dataset No post-translational-modifications are been included in the identified peptides of one dataset. PSI:PI A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet. MS MS:1002865 Accepted manuscript A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet. PSI:PI Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet. MS MS:1002866 Reference Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet. PSI:PI This means that the experimental information available has been improved, for instance precursor charges were added. MS MS:1002867 Experimental information has been refined since this experiment was originally made publicly available This means that the experimental information available has been improved, for instance precursor charges were added. PSI:PI One dataset is not a reanalysis of previously published data. MS MS:1002868 Original data One dataset is not a reanalysis of previously published data. PSI:PI Bioconductor package mzR for reading and writing mass spectrometry data files. MS MS:1002869 mzR Bioconductor package mzR for reading and writing mass spectrometry data files. PSI:PI Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. MS MS:1002870 MSnbase Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. PMID:22113085 Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. MS MS:1002871 CAMERA Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. PMID:22111785 Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002872 Panorama Public dataset identifier Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. MS MS:1002873 Panorama Public dataset URI URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. PSI:PI Thermo Scientific TSQ Altis Triple Quadrupole MS. MS MS:1002874 TSQ Altis Thermo Scientific TSQ Altis Triple Quadrupole MS. PSI:PI Thermo Scientific TSQ Quantis Triple Quadrupole MS. MS MS:1002875 TSQ Quantis Thermo Scientific TSQ Quantis Triple Quadrupole MS. PSI:PI Thermo Scientific TSQ 9000 Triple Quadrupole MS. MS MS:1002876 TSQ 9000 Thermo Scientific TSQ 9000 Triple Quadrupole MS. PSI:PI Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS. MS MS:1002877 Q Exactive HF-X Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS. PSI:PI Software for the analysis of small molecules. MS MS:1002878 small molecule analysis software Software for the analysis of small molecules. PSI:PI Metabolomics analysis software for LC-MS data from Nonlinear Dynamics. MS MS:1002879 Progenesis QI Metabolomics analysis software for LC-MS data from Nonlinear Dynamics. PSI:PI Metabolomics analysis software from Thermo Fisher Scientific. MS MS:1002880 Compound Discoverer Metabolomics analysis software from Thermo Fisher Scientific. PSI:PI Metabolite identification tool MyCompoundID. MS MS:1002881 MyCompoundID Metabolite identification tool MyCompoundID. PMID:23373753 PSI:PI Function used to calculate the study variable quantification value. MS MS:1002882 study variable average function Function used to calculate the study variable quantification value. PSI:PI Median function. MS MS:1002883 median Median function. PSI:PI Function used to calculate the study variable quantification variation value. MS MS:1002884 study variable variation function Function used to calculate the study variable quantification variation value. PSI:PI Standard error function. MS MS:1002885 standard error Standard error function. PSI:PI The value reported in a small molecule quantification. MS MS:1002886 small molecule quantification datatype The value reported in a small molecule quantification. PSI:PI The normalised abundance produced by Progenesis QI LC-MS. MS MS:1002887 Progenesis QI normalised abundance The normalised abundance produced by Progenesis QI LC-MS. PSI:PI The confidence score produced by a small molecule analysis software. MS MS:1002888 small molecule confidence measure The confidence score produced by a small molecule analysis software. PSI:PI The confidence score produced by Progenesis QI. MS MS:1002889 Progenesis MetaScope score The confidence score produced by Progenesis QI. PSI:PI The fragmentation confidence score. MS MS:1002890 fragmentation score The fragmentation confidence score. PSI:PI The isotopic fit confidence score. MS MS:1002891 isotopic fit score The isotopic fit confidence score. PSI:PI An attribute describing ion mobility searches. MS MS:1002892 ion mobility attribute An attribute describing ion mobility searches. PSI:PI Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided. MS MS:1002893 ion mobility array Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided. PSI:PI Unique chemical structure identifier for chemical compounds. MS MS:1002894 InChIKey Unique chemical structure identifier for chemical compounds. PMID:273343401 Compound identification information. MS MS:1002895 small molecule identification attribute Compound identification information. PSI:PI Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'. MS MS:1002896 compound identification confidence level Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'. PMID:29748461 OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'. MS MS:1002897 This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. isotopomer peak true OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'. PSI:PI Native format defined by scan=xsd:nonNegativeInteger. MS MS:1002898 Shimadzu Biotech QTOF nativeID format Native format defined by scan=xsd:nonNegativeInteger. PSI:PI msalign file format. MS MS:1002899 msalign format msalign file format. PSI:MS TopFD feature file format. MS MS:1002900 feature format TopFD feature file format. PSI:MS TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. MS MS:1002901 TopPIC TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. PMID:27423895 http://proteomics.informatics.iupui.edu/software/toppic/index.html Top-down mass spectral feature detection. MS MS:1002902 TopFD Top-down mass spectral feature detection. http://proteomics.informatics.iupui.edu/software/toppic/index.html A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. MS MS:1002903 TopMG A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. PMID:28453668 http://proteomics.informatics.iupui.edu/software/topmg/index.html Proteoform level information. MS MS:1002904 proteoform-level identification attribute Proteoform level information. PSI:PI Identification confidence metric for a proteoform. MS MS:1002905 proteoform-level identification statistic Identification confidence metric for a proteoform. PSI:PI Search engine specific proteoform scores. MS MS:1002906 search engine specific score for proteoforms Search engine specific proteoform scores. PSI:PI Estimation of the global false discovery rate of proteoforms. MS MS:1002907 proteoform-level global FDR Estimation of the global false discovery rate of proteoforms. PSI:PI Estimation of the local false discovery rate of proteoforms. MS MS:1002908 proteoform-level local FDR Estimation of the local false discovery rate of proteoforms. PSI:PI Estimated statistical threshold at proteoform-level. MS MS:1002909 proteoform-level statistical threshold Estimated statistical threshold at proteoform-level. PSI:PI Threshold for the global false discovery rate of proteoforms. MS MS:1002910 proteoform-level global FDR threshold Threshold for the global false discovery rate of proteoforms. PSI:PI Threshold for the local false discovery rate of proteoforms. MS MS:1002911 proteoform-level local FDR threshold Threshold for the local false discovery rate of proteoforms. PSI:PI Search engine input parameters specific to TopPIC. MS MS:1002912 TopPIC input parameter Search engine input parameters specific to TopPIC. PSI:PI Fixed modifications for TopPIC searching. MS MS:1002913 TopPIC:fixed modification Fixed modifications for TopPIC searching. PSI:PI N-terminal forms of proteins allowed in TopPIC searching. MS MS:1002914 TopPIC:N-term form N-terminal forms of proteins allowed in TopPIC searching. PSI:PI Error tolerance for precursor and fragment masses in PPM. MS MS:1002915 TopPIC:error tolerance Error tolerance for precursor and fragment masses in PPM. PSI:PI Maximum value of the mass shift (in Dalton) of an unexpected modification. MS MS:1002916 TopPIC:max shift Maximum value of the mass shift (in Dalton) of an unexpected modification. PSI:PI Minimum value of the mass shift (in Dalton) of an unexpected modification. MS MS:1002917 TopPIC:min shift Minimum value of the mass shift (in Dalton) of an unexpected modification. PSI:PI Maximum number of unexpected modifications in a proteoform spectrum match. MS MS:1002918 TopPIC:shift num Maximum number of unexpected modifications in a proteoform spectrum match. PSI:PI Spectrum-level cutoff type for filtering identified proteoform spectrum matches. MS MS:1002919 TopPIC:spectral cutoff type Spectrum-level cutoff type for filtering identified proteoform spectrum matches. PSI:PI Spectrum-level cutoff value for filtering identified proteoform spectrum matches. MS MS:1002920 TopPIC:spectral cutoff value Spectrum-level cutoff value for filtering identified proteoform spectrum matches. PSI:PI Proteoform-level cutoff type for filtering identified proteoform spectrum matches. MS MS:1002921 TopPIC:proteoform-level cutoff type Proteoform-level cutoff type for filtering identified proteoform spectrum matches. PSI:PI Proteoform-level cutoff value for filtering identified proteoform spectrum matches. MS MS:1002922 TopPIC:proteoform-level cutoff value Proteoform-level cutoff value for filtering identified proteoform spectrum matches. PSI:PI P-value and E-value estimation using generating function. MS MS:1002923 TopPIC:generating function P-value and E-value estimation using generating function. PSI:PI Number of combined spectra. MS MS:1002924 TopPIC:combined spectrum number Number of combined spectra. PSI:PI The text file containing the information of common PTMs. MS MS:1002925 TopPIC:mod file The text file containing the information of common PTMs. PSI:PI Number of threads used in TopPIC. MS MS:1002926 TopPIC:thread number Number of threads used in TopPIC. PSI:PI Proteoform identification using TopFD feature file. MS MS:1002927 TopPIC:use TopFD feature Proteoform identification using TopFD feature file. PSI:PI TopPIC spectrum-level E-value. MS MS:1002928 TopPIC:spectral E-value TopPIC spectrum-level E-value. PSI:PI TopPIC spectrum-level FDR. MS MS:1002929 TopPIC:spectral FDR TopPIC spectrum-level FDR. PSI:PI TopPIC proteoform-level FDR. MS MS:1002930 TopPIC:proteoform-level FDR TopPIC proteoform-level FDR. PSI:PI TopPIC spectrum-level p-value. MS MS:1002931 TopPIC:spectral p-value TopPIC spectrum-level p-value. PSI:PI Modification identification score. MS MS:1002932 TopPIC:MIScore Modification identification score. PMID:27291504 TopPIC:MIScore threshold. MS MS:1002933 TopPIC:MIScore threshold TopPIC:MIScore threshold. PSI:PI Search engine input parameters specific to TopMG. MS MS:1002934 TopMG input parameter Search engine input parameters specific to TopMG. PSI:PI Fixed modifications for TopMG searching. MS MS:1002935 TopMG:fixed modification Fixed modifications for TopMG searching. PSI:PI N-terminal forms of proteins allowed in TopMG searching. MS MS:1002936 TopMG:N-term form N-terminal forms of proteins allowed in TopMG searching. PSI:PI Error tolerance for precursor and fragment masses in PPM. MS MS:1002937 TopMG:error tolerance Error tolerance for precursor and fragment masses in PPM. PSI:PI Maximum value of the mass shift (in Dalton). MS MS:1002938 TopMG:max shift Maximum value of the mass shift (in Dalton). PSI:PI Spectrum-level cutoff type for filtering identified proteoform spectrum matches. MS MS:1002939 TopMG:spectral cutoff type Spectrum-level cutoff type for filtering identified proteoform spectrum matches. PSI:PI Spectrum-level cutoff value for filtering identified proteoform spectrum matches. MS MS:1002940 TopMG:spectral cutoff value Spectrum-level cutoff value for filtering identified proteoform spectrum matches. PSI:PI Proteoform-level cutoff type for filtering identified proteoform spectrum matches. MS MS:1002941 TopMG:proteoform-level cutoff type Proteoform-level cutoff type for filtering identified proteoform spectrum matches. PSI:PI Proteoform-level cutoff value for filtering identified proteoform spectrum matches. MS MS:1002942 TopMG:proteoform-level cutoff value Proteoform-level cutoff value for filtering identified proteoform spectrum matches. PSI:PI The text file containing the information of common PTMs. MS MS:1002943 TopMG:mod file The text file containing the information of common PTMs. PSI:PI Number of threads used in TopMG. MS MS:1002944 TopMG:thread number Number of threads used in TopMG. PSI:PI Proteoform identification using TopFD feature file. MS MS:1002945 TopMG:use TopFD feature Proteoform identification using TopFD feature file. PSI:PI Gap size in constructing proteoform graph. MS MS:1002946 TopMG:proteoform graph gap size Gap size in constructing proteoform graph. PSI:PI Maximum number of variable PTMs. MS MS:1002947 TopMG:variable PTM number Maximum number of variable PTMs. PSI:PI Maximum number of variable PTMs in a proteoform graph gap. MS MS:1002948 TopMG:variable PTM number in proteoform graph gap Maximum number of variable PTMs in a proteoform graph gap. PSI:PI Protein filtering using ASF-DIAGONAL method. MS MS:1002949 TopMG:use ASF-DIAGONAL Protein filtering using ASF-DIAGONAL method. PMID:29327814 TopMG spectrum-level E-value. MS MS:1002950 TopMG:spectral E-value TopMG spectrum-level E-value. PSI:PI TopMG spectrum-level FDR. MS MS:1002951 TopMG:spectral FDR TopMG spectrum-level FDR. PSI:PI TopMG proteoform-level FDR. MS MS:1002952 TopMG:proteoform-level FDR TopMG proteoform-level FDR. PSI:PI TopMG spectrum-level p-value. MS MS:1002953 TopMG:spectral p-value TopMG spectrum-level p-value. PSI:PI Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry. MS MS:1002954 collisional cross sectional area Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry. PSI:PI Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'. MS MS:1002955 hr-ms compound identification confidence level Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'. PMID:24476540 A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'. MS MS:1002956 isotopic ion MS peak A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'. PSI:PI The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'. MS MS:1002957 isotopomer MS peak The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'. PSI:PI The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'. MS MS:1002958 isotopologue MS peak The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'. PSI:PI One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae. MS MS:1002959 isomer One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae. https://goldbook.iupac.org/html/I/I03289.html An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms. MS MS:1002960 isotopomer An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms. https://goldbook.iupac.org/html/I/I03352.html A molecular entity that differs only in isotopic composition (number of isotopic substitutions). MS MS:1002961 isotopologue A molecular entity that differs only in isotopic composition (number of isotopic substitutions). https://goldbook.iupac.org/html/I/I03351.html The arithmetic mean. MS MS:1002962 mean The arithmetic mean. PSI:PI The coefficient of variation. MS MS:1002963 variation coefficient The coefficient of variation. PSI:PI Lipidomics analysis software. MS MS:1002964 lipidomics analysis software Lipidomics analysis software. PSI:PI Lipid Data Analyzer software for lipid quantification. MS MS:1002965 Lipid Data Analyzer Lipid Data Analyzer software for lipid quantification. PMID:29058722 The Lipid Data Analyzer native chrom format. MS MS:1002966 chrom format The Lipid Data Analyzer native chrom format. PSI:PI Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets. MS MS:1002967 LipidHunter Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets. PMID:28753264 Software for consensual cross-platform lipidomics. MS MS:1002968 LipidXplorer Software for consensual cross-platform lipidomics. PMID:22272252 An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. MS MS:1002969 LipidMatch An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. PMID:28693421 Open-source software for automated phospholipid tandem mass spectrometry identification. MS MS:1002970 Greazy Open-source software for automated phospholipid tandem mass spectrometry identification. PMID:27186799 LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library. MS MS:1002971 LipidBlast LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library. PMID:28660581 A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. MS MS:1002972 Lipid-Pro A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. PMID:25433698 A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets. MS MS:1002973 LipidFinder A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets. PMID:28405621 An integrated software package for high-confidence lipid identification. MS MS:1002974 LipiDex An integrated software package for high-confidence lipid identification. PMID:29705063 An-open source software for identifying lipids in LC-MS/MS-based lipidomics data. MS MS:1002975 LIQUID An-open source software for identifying lipids in LC-MS/MS-based lipidomics data. PMID:28158427 Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1). MS MS:1002976 ALEX Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1). PMID:24244551 Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level. MS MS:1002977 ALEX123 Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level. PMID:29786091 Software tool for the quantitative analysis of mass spectrometric lipidome data. MS MS:1002978 LIMSA Software tool for the quantitative analysis of mass spectrometric lipidome data. PMID:17165823 Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers. MS MS:1002979 LOBSTAHS Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers. PMID:27322848 Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species. MS MS:1002980 LipidQA Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species. PMID:17720531 The Proline software suite for mass spectrometry based proteomics. MS MS:1002981 Proline The Proline software suite for mass spectrometry based proteomics. http://www.profiproteomics.fr/proline/ PepNovo tool for de novo peptide sequencing. MS MS:1002982 PepNovo PepNovo tool for de novo peptide sequencing. PMID:15858974 pNovo tool for de novo peptide sequencing and identification using HCD spectra. MS MS:1002983 pNovo pNovo tool for de novo peptide sequencing and identification using HCD spectra. PMID:20329752 Novor real-time peptide de novo sequencing software tool. MS MS:1002984 Novor Novor real-time peptide de novo sequencing software tool. PMID:26122521 Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes. MS MS:1002985 in-gel digestion Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes. PSI:PI Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes. MS MS:1002986 in-solution digestion Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes. PSI:PI IdentiPy. MS MS:1002987 IdentiPy IdentiPy. PMID:29682971 https://bitbucket.org/levitsky/identipy The IdentiPy result 'RHNS'. MS MS:1002988 IdentiPy:RHNS The IdentiPy result 'RHNS'. PSI:PI The IdentiPy result 'hyperscore'. MS MS:1002989 IdentiPy:hyperscore The IdentiPy result 'hyperscore'. PSI:PI ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra. MS MS:1002990 ms_deisotope ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra. https://github.com/mobiusklein/ms_deisotope python-psims, a library for generating mzML and mzIdentML. MS MS:1002991 python-psims python-psims, a library for generating mzML and mzIdentML. https://github.com/mobiusklein/psims Posterior error probability of the best identified peptide of the Andromeda search engine. MS MS:1002995 Andromeda:PEP Posterior error probability of the best identified peptide of the Andromeda search engine. PSI:PI Peak list file format of the Andromeda search engine. MS MS:1002996 Andromeda:apl file format Peak list file format of the Andromeda search engine. PSI:PI Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD). MS MS:1002997 ProteomeXchange dataset identifier reanalysis number Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD). PSI:PI Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS. MS MS:1002998 LCMS-9030 Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS. PSI:MS Shimadzu Scientific Instruments LCMS-8060 MS. MS MS:1002999 LCMS-8060 Shimadzu Scientific Instruments LCMS-8060 MS. PSI:MS Shimadzu Scientific Instruments LCMS-8050 MS. MS MS:1003000 LCMS-8050 Shimadzu Scientific Instruments LCMS-8050 MS. PSI:MS Shimadzu Scientific Instruments LCMS-8045 MS. MS MS:1003001 LCMS-8045 Shimadzu Scientific Instruments LCMS-8045 MS. PSI:MS Shimadzu Scientific Instruments LCMS-8040 MS. MS MS:1003002 LCMS-8040 Shimadzu Scientific Instruments LCMS-8040 MS. PSI:MS Shimadzu Scientific Instruments LCMS-2020. MS MS:1003003 LCMS-2020 Shimadzu Scientific Instruments LCMS-2020. PSI:MS Bruker Daltonics' maXis II. MS MS:1003004 maXis II Bruker Daltonics' maXis II. PSI:MS Bruker Daltonics' timsTOF Pro. MS MS:1003005 timsTOF Pro Bruker Daltonics' timsTOF Pro. PSI:MS Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1003006 mean inverse reduced ion mobility array Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1003007 raw ion mobility array Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1003008 raw inverse reduced ion mobility array Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Shimadzu Biotech LCD file format. MS MS:1003009 Shimadzu Biotech LCD format Shimadzu Biotech LCD file format. PSI:PI Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. MS MS:1003010 LPPtiger Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. PMID:29123162 Sequence-tag-based search engine pFind. MS MS:1003011 pFind Sequence-tag-based search engine pFind. PMID:30295672 Kernel mass spectral dot product scoring function. MS MS:1003012 KSDP score Kernel mass spectral dot product scoring function. PMID:15044235 i3-tms search engine and data-analysis software. MS MS:1003013 i3tms i3-tms search engine and data-analysis software. PSI:PI A database search-based peptide identification tool. MS MS:1003014 MSFragger A database search-based peptide identification tool. PMID:28394336 Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides. MS MS:1003015 razor peptide Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides. PSI:MS Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins. MS MS:1003016 ProteinProphet:peptide weight Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins. PSI:PI Fraction of peptide evidence attributable to a group of proteins. MS MS:1003017 ProteinProphet:peptide group weight Fraction of peptide evidence attributable to a group of proteins. PSI:PI General proteomics processing toolkit for shotgun proteomics. MS MS:1003018 Philosopher General proteomics processing toolkit for shotgun proteomics. https://philosopher.nesvilab.org/ Representation of chromatographic pressure versus time. MS MS:1003019 pressure chromatogram Representation of chromatographic pressure versus time. PSI:MS Representation of the chromatographic flow rate versus time. MS MS:1003020 flow rate chromatogram Representation of the chromatographic flow rate versus time. PSI:MS Post-translational modification which is assumed to be present at each instance of a residue type. MS MS:1003021 Fixed modification Post-translational modification which is assumed to be present at each instance of a residue type. PSI:PI Post-translational modification which may or may not be present at a residue type. MS MS:1003022 Variable modification Post-translational modification which may or may not be present at a residue type. PSI:PI Cross-Linking MS search engine. MS MS:1003023 OpenPepXL Cross-Linking MS search engine. PSI:PI The OpenPepXL score for a crosslink spectrum match. MS MS:1003024 OpenPepXL:score The OpenPepXL score for a crosslink spectrum match. PSI:PI A named element that is an attribute in a proteomics standards file. MS MS:1003025 named element A named element that is an attribute in a proteomics standards file. PSI:PI A named element that is an attribute in a mzIdentML file. MS MS:1003026 named element in mzIdentML A named element that is an attribute in a mzIdentML file. PSI:PI A named element that is an attribute in a mzML file. MS MS:1003027 named element in mzML A named element that is an attribute in a mzML file. PSI:PI Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS. MS MS:1003028 Orbitrap Exploris 480 Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS. PSI:PI Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. MS MS:1003029 Orbitrap Eclipse Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. PSI:PI Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'. MS MS:1003030 Mascot:MinNumSigUniqueSeqs Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'. PSI:PI Main identifier of a CPTAC dataset. MS MS:1003031 CPTAC accession number Main identifier of a CPTAC dataset. PSI:PI The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program. MS MS:1003032 compound identification confidence code in MS-DIAL The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program. PMID:25938372 http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL Non-inherent characteristic attributed to a molecular entity. MS MS:1003033 molecular entity attribute Non-inherent characteristic attributed to a molecular entity. PSI:PI Smallest constituent unit of ordinary matter that constitutes a chemical element. MS MS:1003034 atom Smallest constituent unit of ordinary matter that constitutes a chemical element. https://en.wikipedia.org/wiki/Atom Low molecular weight (< 900 daltons) organic compound that may regulate a biological process. MS MS:1003035 small molecule Low molecular weight (< 900 daltons) organic compound that may regulate a biological process. https://en.wikipedia.org/wiki/Small_molecule Small molecule that is the intermediate end product of metabolism. MS MS:1003036 metabolite Small molecule that is the intermediate end product of metabolism. https://en.wikipedia.org/wiki/Metabolite Nucleotide containing ribose as its pentose component. MS MS:1003037 ribonucleotide Nucleotide containing ribose as its pentose component. https://en.wikipedia.org/wiki/Ribonucleotide Monomer, or single unit, of DNA, or deoxyribonucleic acid. MS MS:1003038 deoxyribonucleotide Monomer, or single unit, of DNA, or deoxyribonucleic acid. https://en.wikipedia.org/wiki/Deoxyribonucleotide Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid. MS MS:1003039 amino acid Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid. https://en.wikipedia.org/wiki/Amino_acid Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule. MS MS:1003040 monosaccharide Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule. https://en.wikipedia.org/wiki/Monosaccharide Molecule composed of a chain of nucleotides. MS MS:1003041 nucleic acid Molecule composed of a chain of nucleotides. https://en.wikipedia.org/wiki/Nucleic_acid Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages. MS MS:1003042 polysaccharide Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages. https://en.wikipedia.org/wiki/Polysaccharide Number of amino acid residues in a peptide, commonly referred to as the peptide length. MS MS:1003043 number of residues Number of amino acid residues in a peptide, commonly referred to as the peptide length. PSI:PI Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not. MS MS:1003044 number of missed cleavages Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not. PSI:PI Process of mapping a peptide sequence to a protein sequence. MS MS:1003045 peptide-to-protein mapping Process of mapping a peptide sequence to a protein sequence. PSI:PI Nonphysical characteristic attributed to the result of peptide-to-protein mapping. MS MS:1003046 peptide-to-protein mapping attribute Nonphysical characteristic attributed to the result of peptide-to-protein mapping. PSI:PI Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence. MS MS:1003047 protein sequence offset Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence. PSI:PI Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules. MS MS:1003048 number of enzymatic termini Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules. PSI:PI Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations. MS MS:1003049 peptidoform Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations. PSI:PI Non-inherent characteristic attributed to a peptidoform. MS MS:1003050 peptidoform attribute Non-inherent characteristic attributed to a peptidoform. PSI:PI Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'. MS parent ion precursor precursor ion MS:1003051 peptidoform ion Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'. PSI:PI Inherent or measurable characteristic of a peptidoform ion. MS MS:1003052 peptidoform ion property Inherent or measurable characteristic of a peptidoform ion. PSI:PI Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents. MS MS:1003053 theoretical monoisotopic m/z Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents. PSI:PI Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes. MS MS:1003054 theoretical average m/z Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes. PSI:PI Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species. MS MS:1003055 adduct Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species. https://en.wikipedia.org/wiki/Adduct Physical measurable characteristic of an adduct ion. MS MS:1003056 adduct ion property Physical measurable characteristic of an adduct ion. PSI:PI Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run. MS MS:1003057 scan number Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run. PSI:PI Inherent or measurable characteristic of a spectrum. MS MS:1003058 spectrum property Inherent or measurable characteristic of a spectrum. PSI:PI Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points. MS MS:1003059 number of peaks Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points. PSI:PI Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks. MS MS:1003060 number of data points Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks. PSI:PI Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection. spectrum name MS MS:1003061 library spectrum name Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection. PSI:PI Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0. MS MS:1003062 library spectrum index Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0. PSI:PI PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library. USI MS MS:1003063 universal spectrum identifier PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library. PSI:PI Non-inherent characteristic attributed to spectrum aggregation. MS MS:1003064 spectrum aggregation attribute Non-inherent characteristic attributed to spectrum aggregation. PSI:PI Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.). MS MS:1003065 spectrum aggregation type Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.). PSI:PI Spectrum that is not the result of some aggregation process. MS MS:1003066 singleton spectrum Spectrum that is not the result of some aggregation process. PSI:PI Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates. MS MS:1003067 consensus spectrum Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates. PSI:PI Spectrum that is considered the most representative from a pool of replicate spectra. MS MS:1003068 best replicate spectrum Spectrum that is considered the most representative from a pool of replicate spectra. PSI:PI Number of replicate spectra available for use during the aggregation process. MS MS:1003069 number of replicate spectra available Number of replicate spectra available for use during the aggregation process. PSI:PI Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm. MS MS:1003070 number of replicate spectra used Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm. PSI:PI Non-inherent characteristic attributed to spectrum aggregation. MS MS:1003071 spectrum origin attribute Non-inherent characteristic attributed to spectrum aggregation. PSI:PI Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.). MS MS:1003072 spectrum origin type Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.). PSI:PI Spectrum that originates from an analysis attempt of a single analyte species on an instrument. MS MS:1003073 observed spectrum Spectrum that originates from an analysis attempt of a single analyte species on an instrument. PSI:PI Spectrum that originates from a compututational algorithm that attempts to predict spectra. MS MS:1003074 predicted spectrum Spectrum that originates from a compututational algorithm that attempts to predict spectra. PSI:PI Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species. MS MS:1003075 demultiplexed spectrum Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species. PSI:PI Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features. MS MS:1003076 uninterpreted spectrum Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features. PSI:PI Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature. MS MS:1003077 interpreted spectrum Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature. PSI:PI Non-inherent characteristic attributed to an interpreted spectrum. MS MS:1003078 interpreted spectrum attribute Non-inherent characteristic attributed to an interpreted spectrum. PSI:PI Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum. MS MS:1003079 total unassigned intensity fraction Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum. PSI:PI Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum. MS MS:1003080 top 20 peak unassigned intensity fraction Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum. PSI:PI Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML. MS MS:1003081 unidentified modification monoisotopic mass delta Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML. PSI:PI Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors. MS MS:1003082 MS-DIAL Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors. PMID:25938372 Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file). MS MS:1003083 raw data file Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file). PSI:MS File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument. MS MS:1003084 processed data file File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument. PSI:MS Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes. MS MS:1003085 previous MSn-1 scan precursor intensity Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes. PSI:MS Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope. MS MS:1003086 precursor apex intensity Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope. PSI:MS Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available. MS MS:1003087 supported by repository but incomplete data and/or metadata Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available. PSI:PI Data array compression using mantissa bit truncation followed by zlib compression. MS MS:1003088 truncation and zlib compression Data array compression using mantissa bit truncation followed by zlib compression. https://github.com/biospi/pwiz Data array compression using mantissa bit truncation, delta prediction and zlib compression. MS MS:1003089 truncation, delta prediction and zlib compression Data array compression using mantissa bit truncation, delta prediction and zlib compression. https://github.com/biospi/pwiz Data array compression using mantissa bit truncation, linear prediction and zlib compression. MS MS:1003090 truncation, linear prediction and zlib compression Data array compression using mantissa bit truncation, linear prediction and zlib compression. https://github.com/biospi/pwiz Settable parameter for a binary data compression event. MS MS:1003091 binary data compression parameter Settable parameter for a binary data compression event. PSI:MS Number of extraneous mantissa bits truncated to improve subsequent compression. MS MS:1003092 number of mantissa bits truncated Number of extraneous mantissa bits truncated to improve subsequent compression. PSI:MS Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues. MS MS:1003093 Lys-N Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues. https://en.wikipedia.org/wiki/Lys-N Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS. MS MS:1003094 Orbitrap Exploris 240 Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS. PSI:PI Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS. MS MS:1003095 Orbitrap Exploris 120 Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS. PSI:PI Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro. MS MS:1003096 LTQ Orbitrap Velos Pro Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro. PSI:MS The probability based MaxQuant protein group score. MS MS:1003097 MaxQuant protein group-level score The probability based MaxQuant protein group score. PSI:MS Peptide probability from Andromeda. MS MS:1003098 Andromeda peptide PEP Peptide probability from Andromeda. PSI:MS Peptide probability from MaxQuant-DIA algorithm. MS MS:1003099 MaxQuant-DIA peptide PEP Peptide probability from MaxQuant-DIA algorithm. PSI:MS PSM evidence score from MaxQuant-DIA algorithm. MS MS:1003100 MaxQuant-DIA score PSM evidence score from MaxQuant-DIA algorithm. PSI:MS PSM evidence PEP probability from MaxQuant-DIA algorithm. MS MS:1003101 MaxQuant-DIA PEP PSM evidence PEP probability from MaxQuant-DIA algorithm. PSI:MS Term for a comment field withing the NIST msp file format MS MS:1003102 NIST msp comment Term for a comment field withing the NIST msp file format PSI:MS Annotation format used for annotating individual spectrum ion peaks. MS MS:1003103 ion annotation format Annotation format used for annotating individual spectrum ion peaks. PSI:MS Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. peptide ion annotation format MS MS:1003104 mzPAF peptide ion annotation format Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. PSI:MS Annotation format designed specifically for crosslinked peptide ion peaks. cross-linked peptide ion annotation format MS MS:1003105 crosslinked peptide ion annotation format Annotation format designed specifically for crosslinked peptide ion peaks. PSI:MS Annotation format designed specifically for glycan ion peaks. MS MS:1003106 glycan ion annotation format Annotation format designed specifically for glycan ion peaks. PSI:MS Annotation format designed specifically for lipid ion peaks. MS MS:1003107 lipid ion annotation format Annotation format designed specifically for lipid ion peaks. PSI:MS PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. MS MS:1003108 PatternLab PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. PSI:MS Identifying crosslinked peptides in complex protein mixtures MS MS:1003109 SIM-XL Identifying crosslinked peptides in complex protein mixtures PSI:MS SIM-XL identification search engine score MS MS:1003110 SIM-XL score SIM-XL identification search engine score PSI:MS Quantification of crosslinked peptides in complex protein mixtures MS MS:1003111 QUIN-XL Quantification of crosslinked peptides in complex protein mixtures PSI:MS Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. MS MS:1003112 Orbitrap ID-X Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. PSI:MS The OpenMS ConsesusID tool posterior error probability MS MS:1003113 OpenMS:ConsensusID PEP The OpenMS ConsesusID tool posterior error probability PSI:MS The score of the best PSM selected by the underlying identification tool MS MS:1003114 OpenMS:Best PSM Score The score of the best PSM selected by the underlying identification tool PSI:MS The OpenMS Target-decoy q-values at PSM level MS MS:1003115 OpenMS:Target-decoy PSM q-value The OpenMS Target-decoy q-values at PSM level PSI:MS The OpenMS Target-decoy q-values at peptide sequence level MS MS:1003116 OpenMS:Target-decoy peptide q-value The OpenMS Target-decoy q-values at peptide sequence level PSI:MS The OpenMS Target-decoy q-values at protein level MS MS:1003117 OpenMS:Target-decoy protein q-value The OpenMS Target-decoy q-values at protein level PSI:MS A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework MS MS:1003118 EPIFANY A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework PSI:MS Protein Posterior probability calculated by EPIFANY protein inference algorithm MS MS:1003119 EPIFANY:Protein posterior probability Protein Posterior probability calculated by EPIFANY protein inference algorithm PSI:MS The data type LFQ intensity produced by OpenMS. MS MS:1003120 OpenMS:LFQ intensity The data type LFQ intensity produced by OpenMS. PSI:MS The data type LFQ spectral count produced by OpenMS. MS MS:1003121 OpenMS:LFQ spectral count The data type LFQ spectral count produced by OpenMS. PSI:MS Bruker Daltonics' rapiflex: MALDI TOF/TOF. MS MS:1003122 rapifleX Bruker Daltonics' rapiflex: MALDI TOF/TOF. PSI:MS Bruker Daltonics timsTOF series MS MS:1003123 Bruker Daltonics timsTOF series Bruker Daltonics timsTOF series PSI:MS Bruker Daltonics' timsTOF fleX MS MS:1003124 timsTOF fleX Bruker Daltonics' timsTOF fleX PSI:MS ProSight spectrum-level Q-value. MS MS:1003125 ProSight:spectral Q-value ProSight spectrum-level Q-value. PSI:MS ProSight spectrum-level P-score. MS MS:1003126 ProSight:spectral P-score ProSight spectrum-level P-score. PSI:MS ProSight spectrum-level E-value. MS MS:1003127 ProSight:spectral E-value ProSight spectrum-level E-value. PSI:MS ProSight spectrum-level C-score. MS MS:1003128 ProSight:spectral C-score ProSight spectrum-level C-score. PSI:MS Estimation of the Q-value for proteoforms. MS MS:1003129 proteoform-level Q-value Estimation of the Q-value for proteoforms. PSI:MS ProSight proteoform-level Q-value. MS MS:1003130 ProSight:proteoform Q-value ProSight proteoform-level Q-value. PSI:MS Isoform level information. MS MS:1003131 isoform-level identification attribute Isoform level information. PSI:MS Identification confidence metric for a isoform. MS MS:1003132 isoform-level identification statistic Identification confidence metric for a isoform. PSI:MS Estimation of the Q-value for isoforms. MS MS:1003133 isoform-level Q-value Estimation of the Q-value for isoforms. PSI:MS ProSight isoform-level Q-value. MS MS:1003134 ProSight:isoform Q-value ProSight isoform-level Q-value. PSI:MS ProSight protein-level Q-value. MS MS:1003135 ProSight:protein Q-value ProSight protein-level Q-value. PSI:MS Search engine input parameters specific to ProSight. MS MS:1003136 ProSight input parameter Search engine input parameters specific to ProSight. PSI:MS Search engine input parameters specific to TDPortal. MS MS:1003137 TDPortal input parameter Search engine input parameters specific to TDPortal. PSI:MS If true, runs delta m mode in ProSight. MS MS:1003138 ProSight:Run delta m mode If true, runs delta m mode in ProSight. PSI:MS If true, runs Subsequence Search mode in ProSight. MS MS:1003139 ProSight:Run Subsequence Search mode If true, runs Subsequence Search mode in ProSight. PSI:MS If true, runs Annotated Proteoform Search mode in ProSight. MS MS:1003140 ProSight:Run Annotated Proteoform Search mode If true, runs Annotated Proteoform Search mode in ProSight. PSI:MS ProSight: Database search engine for top-down proteomics. MS MS:1003141 ProSight ProSight: Database search engine for top-down proteomics. PSI:MS TDPortal: Database search engine for top-down proteomics. MS MS:1003142 TDPortal TDPortal: Database search engine for top-down proteomics. PSI:MS A data array of mass values. binary-data-type:MS:1000521 binary-data-type:MS:1000523 MS MS:1003143 mass array A data array of mass values. PSI:MS binary-data-type:MS:1000521 32-bit float binary-data-type:MS:1000523 64-bit float SCIEX Triple Quad 7500. MS MS:1003144 Triple Quad 7500 SCIEX Triple Quad 7500. PSI:MS Cross-platform software to convert Thermo RAW files to a number of open formats. MS MS:1003145 ThermoRawFileParser Cross-platform software to convert Thermo RAW files to a number of open formats. DOI:10.1021/acs.jproteome.9b00328 PMID:31755270 Python module that helps handling various proteomics data analysis tasks. MS MS:1003146 pyteomics Python module that helps handling various proteomics data analysis tasks. DOI:10.1021/acs.jproteome.8b00717 PMID:30576148 Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet. MS MS:1003147 PTMProphet probability Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet. DOI:10.1021/acs.jproteome.9b00205 PMID:31290668 PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet. MS MS:1003148 PTMProphet mean best probability PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet. DOI:10.1021/acs.jproteome.9b00205 PMID:31290668 PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type. MS MS:1003149 PTMProphet normalized information content PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type. DOI:10.1021/acs.jproteome.9b00205 PMID:31290668 PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type. MS MS:1003150 PTMProphet information content PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type. DOI:10.1021/acs.jproteome.9b00205 PMID:31290668 SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. MS MS:1003151 SHA-256 SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. PSI:MS Shimadzu Scientific Instruments GCMS-QP2010SE. MS MS:1003152 GCMS-QP2010SE Shimadzu Scientific Instruments GCMS-QP2010SE. PSI:MS Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1003153 raw ion mobility drift time array Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1003154 deconvoluted ion mobility array Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1003155 deconvoluted inverse reduced ion mobility array Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. MS MS:1003156 deconvoluted ion mobility drift time array Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. PSI:MS Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum. MS MS:1003157 scanning quadrupole position lower bound m/z array Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum. PSI:MS Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum. MS MS:1003158 scanning quadrupole position upper bound m/z array Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum. PSI:MS Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range. MS MS:1003159 isolation window full range Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range. PSI:MS Proteomics Standards Initiative mzQC format for quality control data. MS MS:1003160 mzQC format Proteomics Standards Initiative mzQC format for quality control data. PSI:MS Grouping term for quality control data formats. MS MS:1003161 quality control data format Grouping term for quality control data formats. PSI:MS Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization. PTXQC MS MS:1003162 PTX-QC Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization. DOI:10.1021/acs.jproteome.5b00780 PMID:26653327 https://github.com/cbielow/PTXQC/ The set of analyte identifiers that compose an interpretation of a spectrum. MS MS:1003163 analyte mixture members The set of analyte identifiers that compose an interpretation of a spectrum. PSI:PI QuaMeter IDFree software for QC metric calculation. QuaMeter MS MS:1003164 QuaMeter IDFree QuaMeter IDFree software for QC metric calculation. DOI:10.1021/ac4034455 PMID:24494671 iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files. MS MS:1003165 iMonDB iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files. DOI:10.1021/acs.jproteome.5b00127 PMID:25798920 https://github.com/bittremieux/iMonDB Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum MS MS:1003166 assigned intensity fraction Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum PSI:PI The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte MS MS:1003167 MSn-1 isolation window precursor purity The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte PSI:PI A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools. MS MS:1003168 library spectrum comment A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools. PSI:PI Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation MS MS:1003169 proforma peptidoform sequence Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation PSI:PI A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments MS MS:1003170 spectral library A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments PSI:PI An attribute of a spectral library MS MS:1003171 spectral library attribute An attribute of a spectral library PSI:PI An entry in a spectral library representing a spectrum MS MS:1003172 library spectrum An entry in a spectral library representing a spectrum PSI:PI An attribute that takes on a numeric value MS MS:1003173 numeric attribute An attribute that takes on a numeric value PSI:PI The maximum value for this attribute MS MS:1003174 attribute maximum The maximum value for this attribute PSI:PI The minimum value for this attribute MS MS:1003175 attribute minimum The minimum value for this attribute PSI:PI The arithmetic mean value for this attribute MS MS:1003176 attribute mean The arithmetic mean value for this attribute PSI:PI The standard deviation (exact value of population, or estimate from sample) of this attribute MS MS:1003177 attribute standard deviation The standard deviation (exact value of population, or estimate from sample) of this attribute PSI:PI The coefficient of variation of this attribute, i.e. standard deviation divided by the mean MS MS:1003178 attribute coefficient of variation The coefficient of variation of this attribute, i.e. standard deviation divided by the mean PSI:PI The most appropriate summary value of the attribute, usually but not necessarily the mean MS MS:1003179 attribute summary value The most appropriate summary value of the attribute, usually but not necessarily the mean PSI:PI The median of this attribute MS MS:1003180 attribute median The median of this attribute PSI:PI Combination of two or more dissociation methods that are known by a special term. MS MS:1003181 combined dissociation method Combination of two or more dissociation methods that are known by a special term. PSI:PI Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID). ETciD MS MS:1003182 electron-transfer/collision-induced dissociation Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID). PSI:PI Waters oa-ToF based Synapt XS. MS MS:1003183 Synapt XS Waters oa-ToF based Synapt XS. PSI:PI Waters oa-ToF based SELECT SERIES Cyclic IMS. MS MS:1003184 SELECT SERIES Cyclic IMS Waters oa-ToF based SELECT SERIES Cyclic IMS. PSI:PI Waters oa-ToF based SELECT SERIES MRT. MS MS:1003185 SELECT SERIES MRT Waters oa-ToF based SELECT SERIES MRT. PSI:PI Version number of the [PSI] library format specification MS MS:1003186 library format version Version number of the [PSI] library format specification PSI:PI Short identifier for the library for easy reference, preferably but not necessarily globally unique MS MS:1003187 library identifier Short identifier for the library for easy reference, preferably but not necessarily globally unique PSI:PI A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library. MS MS:1003188 library name A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library. PSI:PI Extended free-text description of the library MS MS:1003189 library description Extended free-text description of the library PSI:PI Version number of the library, usually refering to a certain release of a continually updated library MS MS:1003190 library version Version number of the library, usually refering to a certain release of a continually updated library PSI:PI URI or URL that uniquely identifies the library MS MS:1003191 library URI URI or URL that uniquely identifies the library PSI:PI A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching MS MS:1003192 decoy spectrum A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching PSI:PI A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence. MS MS:1003193 shuffle-and-reposition decoy spectrum A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence. PSI:PI A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum. MS MS:1003194 precursor shift decoy spectrum A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum. PSI:PI A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform MS MS:1003195 unnatural peptidoform decoy spectrum A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform PSI:PI A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample MS MS:1003196 unrelated species decoy spectrum A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample PSI:PI URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/) MS MS:1003197 license URI URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/) PSI:PI Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work MS MS:1003198 copyright notice Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work PSI:PI Extended free-text description of the difference from the previous version MS MS:1003199 change log Extended free-text description of the difference from the previous version PSI:PI Version number of the software package used for library creation MS MS:1003200 software version Version number of the software package used for library creation PSI:PI Abstract term containing several different types of provenance information MS MS:1003201 library provenance attribute Abstract term containing several different types of provenance information PSI:PI A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington MS MS:1003202 BiblioSpec A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington PSI:PI Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible. MS MS:1003203 constituent spectrum file Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible. PSI:PI Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible MS MS:1003204 constituent identification file Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible PSI:PI Source library URI which(at least) a subset of spectra were extracted from. MS MS:1003205 constituent library file Source library URI which(at least) a subset of spectra were extracted from. PSI:PI String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped MS MS:1003206 library creation log String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped PSI:PI Library creation software MS MS:1003207 library creation software Library creation software PSI:MS The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum. MS MS:1003208 experimental precursor monoisotopic m/z The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum. PSI:MS The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum. MS MS:1003209 monoisotopic m/z deviation The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum. PSI:MS The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum. MS MS:1003210 average m/z deviation The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum. PSI:MS A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library MS MS:1003211 library spectrum attribute set A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library PSI:PI A name to refer to a library attribute set MS MS:1003212 library attribute set name A name to refer to a library attribute set PSI:PI Mode of running a mass spectrometer method by which mass ranges are selected and possibly dissociated. MS MS:1003213 mass spectrometry acquisition method Mode of running a mass spectrometer method by which mass ranges are selected and possibly dissociated. PSI:MS Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated. MS MS:1003214 mass spectrometry acquisition method aspect Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated. PSI:MS Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions. DIA MS MS:1003215 data-independent acquisition Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions. PSI:MS Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.. MS MS:1003216 dissociation of full mass range Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.. PSI:MS Mass spectrometer data acquisition method wherein ????. MS MS:1003217 dissociation of scanning quadrupole across a specified mass range Mass spectrometer data acquisition method wherein ????. PSI:MS Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured. MS MS:1003218 dissociation of sequential mass ranges Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured. PSI:MS Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement. MS MS:1003219 ion mobility separation Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement. PSI:MS Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule. MS MS:1003220 adduct deconvolution Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule. PSI:MS Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run. DDA MS MS:1003221 data-dependent acquisition Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run. PSI:MS Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte. MS MS:1003222 ion mobility deconvolution Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte. PSI:MS Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC. MS MS:1003224 data independent acquisition from dissociation of sequential mass ranges Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC. PSI:MS Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF. MS MS:1003225 data independent acquisition from dissociation of sequential mass ranges after ion mobility separation Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF. PSI:MS Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF. MS MS:1003226 data independent acquisition from dissociation of full mass range after ion mobility separation Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF. PSI:MS Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID. MS MS:1003227 data independent acquisition from dissociation of full mass range Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID. PSI:MS Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR. MS MS:1003228 data independent acquisition from dissociation of scanning quadrupole across mass range Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR. PSI:MS Bruker Daltonics' timsTOF. MS MS:1003229 timsTOF Bruker Daltonics' timsTOF. PSI:MS Bruker Daltonics' timsTOF Pro 2. MS MS:1003230 timsTOF Pro 2 Bruker Daltonics' timsTOF Pro 2. PSI:MS Bruker Daltonics' timsTOF SCP. MS MS:1003231 timsTOF SCP Bruker Daltonics' timsTOF SCP. PSI:MS comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB). MS MS:1003232 PeakForest comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB). https://peakforest.org/ An attribute that describes information about an entry in a spectral library MS MS:1003234 library spectrum attribute An attribute that describes information about an entry in a spectral library PSI:PI The ionization of analytes from a piece of paper by applying a solvent and voltage. MS MS:1003235 paper spray ionization The ionization of analytes from a piece of paper by applying a solvent and voltage. PSI:MS An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library. MS MS:1003237 library spectrum key An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library. PSI:PI A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library MS MS:1003238 library analyte attribute set A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library PSI:PI A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library MS MS:1003239 library interpretation attribute set A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library PSI:PI A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores MS MS:1003240 peak intensity transform A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores PSI:PI A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots MS MS:1003241 square root transform A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots PSI:PI A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks MS MS:1003242 rank transform A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks PSI:PI The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's mass plus the mass of a proton) MS MS:1003243 adduct ion mass The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's mass plus the mass of a proton) PSI:PI Accession number (e.g. in PeptideAtlas) of the peptide sequence MS MS:1003244 peptide accession number Accession number (e.g. in PeptideAtlas) of the peptide sequence PSI:PI Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS. MS MS:1003245 Q Exactive UHMR Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS. PSI:PI Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons. UVPD MS MS:1003246 ultraviolet photodissociation Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons. PSI:MS A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation. NETD MS MS:1003247 negative electron transfer dissociation A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation. DOI:10.1016/j.jasms.2005.01.015 PSI:MS Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation. PTR MS MS:1003248 proton transfer reaction Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation. DOI:10.1002/mas.20048 PSI:MS Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte. PTCR MS MS:1003249 proton transfer charge reduction Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte. PSI:MS The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence. MS MS:1003250 count of identified peptidoforms The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence. PSI:PI The number of spectra that pass the threshold to be considered identified with sufficient confidence. MS MS:1003251 count of identified spectra The number of spectra that pass the threshold to be considered identified with sufficient confidence. PSI:PI Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer. MS MS:1003252 Xevo G2-XS QTof Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer. PSI:PI A universal software for data-independent acquisition (DIA) proteomics data processing MS MS:1003253 DIA-NN A universal software for data-independent acquisition (DIA) proteomics data processing PMID:31768060 https://github.com/vdemichev/DiaNN An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. MS MS:1003254 peak attribute An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. PSI:PI For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. MS MS:1003255 pre-decharged charge state For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. PSI:PI Non-inherent characteristic attributed to a peptidoform MS MS:1003256 peptidoform ion attribute Non-inherent characteristic attributed to a peptidoform PSI:PI A link from one spectrum to another spectrum of interest MS MS:1003257 library spectrum cross reference A link from one spectrum to another spectrum of interest PSI:PI A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. MS MS:1003258 related spectrum A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. PSI:PI A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. MS MS:1003259 related spectrum keys A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. PSI:PI A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier MS MS:1003260 related spectrum USI A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier PSI:PI A free-text string describing the related spectrum and/or its relationship to this spectrum MS MS:1003261 related spectrum description A free-text string describing the related spectrum and/or its relationship to this spectrum PSI:PI A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion. MS MS:1003262 similar spectrum A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion. PSI:PI A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. MS MS:1003263 similar spectrum keys A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. PSI:PI A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier MS MS:1003264 similar spectrum USI A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier PSI:PI A group of spectra that are spectrally similar to each other MS MS:1003265 spectrum cluster A group of spectra that are spectrally similar to each other PSI:PI A non-inherent characteristic of a spectrum cluster MS MS:1003266 spectrum cluster attribute A non-inherent characteristic of a spectrum cluster PSI:PI An ordinal number uniquely identifying a spectrum cluster. It should start with 1. MS MS:1003267 spectrum cluster key An ordinal number uniquely identifying a spectrum cluster. It should start with 1. PSI:PI A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library. MS MS:1003268 spectrum cluster member spectrum keys A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library. PSI:PI A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier. MS MS:1003269 spectrum cluster member USI A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier. PSI:PI A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type. MS MS:1003270 proforma peptidoform ion notation A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type. PSI:PI The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum. MS MS:1003271 peak annotation The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum. PSI:PI A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'. MS MS:1003272 peak annotation string A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'. PSI:PI A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'. MS MS:1003273 peak annotation confidence A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'. PSI:PI A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1. MS MS:1003274 peak annotation confidence metric A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1. PSI:PI A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value MS MS:1003275 other attribute name A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value PSI:MS A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name MS MS:1003276 other attribute value A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name PSI:MS Value range for signed normalized score values. MS MS:1003277 value between -1 and 1 inclusive Value range for signed normalized score values. PSI:PI A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte. MS MS:1003278 m/z variability of peak A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte. PSI:PI The frequency at which this peak is observed among replicate spectra of the same analyte. MS MS:1003279 observation frequency of peak The frequency at which this peak is observed among replicate spectra of the same analyte. PSI:PI A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte. MS MS:1003280 intensity variability of peak A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte. PSI:PI Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/. MS MS:1003281 Casanovo Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/. https://github.com/Noble-Lab/casanovo/ Bruker TSF raw file format. MS MS:1003282 Bruker TSF format Bruker TSF raw file format. PSI:MS Native format defined by frame=xsd:nonNegativeInteger. MS MS:1003283 Bruker TSF nativeID format Native format defined by frame=xsd:nonNegativeInteger. PSI:MS Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation. MS MS:1003284 Bruker TSF nativeID format, combined spectra Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation. PSI:PI The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte. MS MS:1003285 standard deviation of m/z values of peak among replicates The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte. PSI:PI The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte. MS MS:1003286 coefficient of variation of intensity of peak among replicates The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte. PSI:PI The standard deviation of the intensities of this peak among the replicate spectra of the same analyte. MS MS:1003287 standard deviation of intensity of peak among replicates The standard deviation of the intensities of this peak among the replicate spectra of the same analyte. PSI:PI The number of unassigned peaks in the spectrum. MS MS:1003288 number of unassigned peaks The number of unassigned peaks in the spectrum. NIST The intensity of the highest unassigned peak in the spectrum. MS MS:1003289 intensity of highest unassigned peak The intensity of the highest unassigned peak in the spectrum. NIST The number of unassigned peaks among the most intense 20 peaks in the spectrum. MS MS:1003290 number of unassigned peaks among top 20 peaks The number of unassigned peaks among the most intense 20 peaks in the spectrum. NIST Luciphor phosphosite localization score MS MS:1003291 Luciphor deltaScore Luciphor phosphosite localization score PSI:MS Thermo Scientific TSQ Altis Plus Triple Quadrupole MS. MS MS:1003292 TSQ Altis Plus Thermo Scientific TSQ Altis Plus Triple Quadrupole MS. PSI:PI SCIEX ZenoTOF 7600. MS MS:1003293 ZenoTOF 7600 SCIEX ZenoTOF 7600. PSI:MS A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. EAD MS MS:1003294 electron activated dissociation A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. PSI:MS Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum. MS MS:1003295 summary statistics of replicates Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum. PSI:PI The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name' MS MS:1003296 number of replicates spectra used from source The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name' PSI:PI A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum. MS MS:1003297 contributing replicate spectrum A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum. PSI:PI A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys. MS MS:1003298 contributing replicate spectrum keys A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys. PSI:PI A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers. MS MS:1003299 contributing replicate spectrum USI A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers. PSI:PI Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte. MS MS:1003300 spectrum match Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte. PSI:PI Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence. PSM MS MS:1003301 peptide-spectrum match Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence. PSI:PI Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering. SSM MS MS:1003302 spectrum-spectrum match Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering. PSI:PI A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone. MS MS:1003303 spectral similarity A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone. PSI:PI The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity. cosine similarity MS MS:1003304 spectral dot product The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity. PSI:PI The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space. MS MS:1003305 spectral Euclidean distance The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space. PSI:PI The number of peaks with closely matching m/z values that are common to two spectra. MS MS:1003306 shared peak count The number of peaks with closely matching m/z values that are common to two spectra. PSI:PI The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi. MS MS:1003307 normalized spectral angle The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi. https://doi.org/10.1074/mcp.O113.036475 The Pearson's rho statistic between a pair of points representing two vectorized spectra. MS MS:1003308 spectral Pearson correlation The Pearson's rho statistic between a pair of points representing two vectorized spectra. PSI:PI The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature. MS MS:1003309 Goslin The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature. PMID:32589019 https://github.com/lifs-tools/goslin Identification confidence levels based on the updated lipid shorthand nomenclature. The value slot can have the values 'Category', 'Class', 'Species', 'Phosphate-position', 'Molecular species', 'sn-position', 'DBE position', 'Structure defined', 'Full structure', 'Complete structure'. MS MS:1003310 Lipid shorthand identification confidence level Identification confidence levels based on the updated lipid shorthand nomenclature. The value slot can have the values 'Category', 'Class', 'Species', 'Phosphate-position', 'Molecular species', 'sn-position', 'DBE position', 'Structure defined', 'Full structure', 'Complete structure'. PMID:33037133 The lipid empirical score is a point-based lipid class-specific scoring system based on MS and other evidence sources as defined by the Lipidomics Standards Initiative (LSI). The score has a numeric value between 0 and 100. Score values are lipid class-specific and are therefore not immediately comparable between lipid classes. MS MS:1003311 Lipid empirical score Lipid shorthand identification confidence level 'Category'. MS MS:1003312 Lipid shorthand identification confidence - Category Lipid shorthand identification confidence level 'Category'. PMID:33037133 Lipid shorthand identification confidence level 'Class'. MS MS:1003313 Lipid shorthand identification confidence - Class Lipid shorthand identification confidence level 'Class'. PMID:33037133 Lipid shorthand identification confidence level 'Species'. MS MS:1003314 Lipid shorthand identification confidence - Species Lipid shorthand identification confidence level 'Species'. PMID:33037133 Lipid shorthand identification confidence level 'Phosphate-position'. MS MS:1003315 Lipid shorthand identification confidence - Phosphate-position Lipid shorthand identification confidence level 'Phosphate-position'. PMID:33037133 Lipid shorthand identification confidence level 'Molecular species'. MS MS:1003316 Lipid shorthand identification confidence - Molecular species Lipid shorthand identification confidence level 'Molecular species'. PMID:33037133 Lipid shorthand identification confidence level 'sn-position'. MS MS:1003317 Lipid shorthand identification confidence - sn-position Lipid shorthand identification confidence level 'sn-position'. PMID:33037133 Lipid shorthand identification confidence level 'DBE pos'. MS MS:1003318 Lipid shorthand identification confidence - DBE pos Lipid shorthand identification confidence level 'DBE pos'. PMID:33037133 Lipid shorthand identification confidence level 'Structure defined'. MS MS:1003319 Lipid shorthand identification confidence - Structure defined Lipid shorthand identification confidence level 'Structure defined'. PMID:33037133 The number of spectra in a spectrum cluster. MS MS:1003320 spectrum cluster size The number of spectra in a spectrum cluster. PSI:PI Summary statistics of an attribute among all spectra of a spectrum cluster. MS MS:1003321 summary statistics of clustered spectra Summary statistics of an attribute among all spectra of a spectrum cluster. PSI:PI Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not. MS MS:1003322 spectrum cluster best representative Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not. PSI:PI Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not. MS MS:1003323 spectrum cluster consensus spectrum Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not. PSI:PI Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum. MS MS:1003324 spectral dot product to aggregated spectrum Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum. PSI:PI Lipid shorthand identification confidence level 'Full structure'. MS MS:1003325 Lipid shorthand identification confidence - Full structure Lipid shorthand identification confidence level 'Full structure'. PMID:33037133 Lipid shorthand identification confidence level 'Complete structure'. MS MS:1003326 Lipid shorthand identification confidence - Complete structure Lipid shorthand identification confidence level 'Complete structure'. PMID:33037133 The number of protein groups that pass the threshold to be considered identified with sufficient confidence. MS MS:1003327 number of identified protein groups The number of protein groups that pass the threshold to be considered identified with sufficient confidence. PSI:PI The number of proteoforms that pass the threshold to be considered identified with sufficient confidence. MS MS:1003328 number of identified proteoforms The number of proteoforms that pass the threshold to be considered identified with sufficient confidence. PSI:PI Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink. loop-link spectrum identification item MS MS:1003329 looplink spectrum identification item Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink. PSI:MS Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions. MS MS:1003330 noncovalently associated peptides search Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions. PSI:MS Noncovalently associated peptides spectrum identification item. MS MS:1003331 noncovalently associated peptides spectrum identification item Noncovalently associated peptides spectrum identification item. PSI:MS Provides an identifier to encode identifications based on multiple spectra. MS MS:1003332 identification based on multiple spectra Provides an identifier to encode identifications based on multiple spectra. PSI:MS ^(?<MULTIPLE_SPECTRA_IDENTIFIER>[0-9]+)(?::(?<PARENT_OR_CHILD>P|C))?$ MS MS:1003333 regular expression for encoding identifications based on multiple spectra. ^(?<MULTIPLE_SPECTRA_IDENTIFIER>[0-9]+)(?::(?<PARENT_OR_CHILD>P|C))?$ PSI:MS Parent term for PSM-level scores for identifications based on multiple spectra. MS MS:1003334 parent term for PSM-level scores for identifications based on multiple spectra Parent term for PSM-level scores for identifications based on multiple spectra. PSI:MS ^(?<MULTIPLE_SPECTRA_IDENTIFIER>[0-9]+):(?<SCORE>[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+))$ MS MS:1003335 regular expression for PSM-level scores for identifications based on multiple spectra ^(?<MULTIPLE_SPECTRA_IDENTIFIER>[0-9]+):(?<SCORE>[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+))$ PSI:MS PEP score for identifications based on multiple spectra. MS MS:1003336 posterior error probability from identification based on multiple spectra PEP score for identifications based on multiple spectra. PSI:MS Estimation of the global false discovery rate of crosslinked peptide spectrum matches. MS MS:1003337 crosslinked PSM-level global FDR Estimation of the global false discovery rate of crosslinked peptide spectrum matches. PSI:MS Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides. MS MS:1003338 peptide-pair sequence-level global FDR Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides. PSI:MS Peptide-pair passes threshold. Applicable in the case of crosslinked peptides or noncovalently associated peptides. MS MS:1003339 peptide-pair passes threshold Peptide-pair passes threshold. Applicable in the case of crosslinked peptides or noncovalently associated peptides. PSI:MS Residue-pair passes threshold. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI). MS MS:1003340 residue-pair passes threshold Residue-pair passes threshold. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI). PSI:MS Protein-protein interaction passes threshold. MS MS:1003341 protein-protein interaction passes threshold Protein-protein interaction passes threshold. PSI:MS ^((?<int_ID>[0-9]+):(?<PASS_THRESHOLD>true|false))$ MS MS:1003342 regular expression for whether interaction score derived from crosslinking passes threshold ^((?<int_ID>[0-9]+):(?<PASS_THRESHOLD>true|false))$ PSI:MS States whether FDR was applied separately to self crosslinks (crosslinks between peptides within one protein sequence) and protein heteromeric crosslinks (crosslinks between distinct protein sequences). MS MS:1003343 FDR applied separately to self crosslinks and protein heteromeric crosslinks States whether FDR was applied separately to self crosslinks (crosslinks between peptides within one protein sequence) and protein heteromeric crosslinks (crosslinks between distinct protein sequences). PSI:MS Reference to a residue-pair supported by this identification item, the value is the identifier for the residue-pair. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI). MS MS:1003344 residue-pair ref Reference to a residue-pair supported by this identification item, the value is the identifier for the residue-pair. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI). PSI:MS ^(([0-9]+).(a|b))$ MS MS:1003345 regular expression for residue-pair ref ^(([0-9]+).(a|b))$ PSI:MS This term indicates that a given protein modification is a derivative of a cleavable crosslinker. MS MS:1003346 cleavable crosslinker stub This term indicates that a given protein modification is a derivative of a cleavable crosslinker. PSI:MS The single letter code in Unimod that identifies a specific derivative of a modification. For example, in UNIMOD:1842 (http://www.unimod.org/modifications_view.php?editid1=1842) the letter ‘W’ represents the derivative ‘water quenched monolink’. MS MS:1003347 Unimod derivative code The single letter code in Unimod that identifies a specific derivative of a modification. For example, in UNIMOD:1842 (http://www.unimod.org/modifications_view.php?editid1=1842) the letter ‘W’ represents the derivative ‘water quenched monolink’. PSI:MS large-scale study of proteins and proteomes. MS MS:1003348 proteomics large-scale study of proteins and proteomes. PSI:MS large-scale study of proteins and proteomes via the use of affinity reagents. MS MS:1003349 affinity proteomics large-scale study of proteins and proteomes via the use of affinity reagents. PSI:MS large-scale study of proteins and proteomes via the use of mass spectrometers to measure the masses and abundances of charged proteins or protein fragments. MS MS:1003350 mass spectrometry proteomics large-scale study of proteins and proteomes via the use of mass spectrometers to measure the masses and abundances of charged proteins or protein fragments. PSI:MS study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact proteins. MS MS:1003351 top-down proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact proteins. PSI:MS study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact folded proteins. MS MS:1003352 native top-down proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact folded proteins. PSI:MS study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact denatured proteins. MS MS:1003353 non-native top-down proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact denatured proteins. PSI:MS study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins. MS MS:1003354 middle-down proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins. PSI:MS study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins. MS MS:1003355 bottom-up proteomics study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins. PSI:MS Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. MS MS:1003356 Orbitrap Ascend Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. PSI:PI ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart. MS MS:1003357 ANN-SoLo ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart. doi:10.1021/acs.jproteome.8b00359 doi:10.1021/acs.jproteome.9b00291 The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score. MS MS:1003358 XCorr rank The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score. PSI:MS A p-value for the XCorr score, calculated using dynamic programming. MS MS:1003359 exact p-value A p-value for the XCorr score, calculated using dynamic programming. PMID:24895379 A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum. MS MS:1003360 refactored XCorr A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum. PMID:30221945 The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks. MS MS:1003361 res-ev score The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks. PMID:30221945 The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score. MS MS:1003362 res-ev rank The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score. PMID:30221945 The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure. MS MS:1003363 res-ev p-value The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure. PMID:30221945 A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them. MS MS:1003364 combined p-value A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them. PMID:30221945 The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value. MS MS:1003365 combined p-value rank The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value. PMID:30221945 A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum. MS MS:1003366 tailor score A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum. PMID:32175744 The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution. MS MS:1003367 monoisotopic mass deisotoping The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution. PSI:MS The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution. MS MS:1003368 most abundant mass deisotoping The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution. PSI:MS The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution. MS MS:1003369 average mass deisotoping The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution. PSI:MS The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z. MS MS:1003370 reduction to summed singly charged peak list The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z. PSI:MS The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer. MS MS:1003371 SelexION compensation voltage The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer. PSI:MS The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file. MS MS:1003372 specification document extension version The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file. PSI:MS The versioning of an mzIdentML extension document. MS MS:1003373 mzIdentML extension version The versioning of an mzIdentML extension document. PSI:PI ChemClipse/OpenChrom file format. MS MS:1003374 Open Chromatography Binary OCB format ChemClipse/OpenChrom file format. PSI:MS Conversion of a file format to Open Chromatography Binary OCB file format. MS MS:1003375 Conversion to OCB Conversion of a file format to Open Chromatography Binary OCB file format. PSI:MS ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH. chemclipse MS MS:1003376 ChemClipse ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH. https://projects.eclipse.org/projects/science.chemclipse OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse. openchrom MS MS:1003377 OpenChrom OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse. DOI:10.1186/1471-2105-11-405 PMID:20673335 https://www.openchrom.net/ Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer. MS MS:1003378 Orbitrap Astral Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer. PSI:MS A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution. Astral MS MS:1003379 asymmetric track lossless time-of-flight analyzer A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution. PSI:MS Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer. MS MS:1003380 Xevo G3 QTof Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer. PSI:MS Waters Corporation RDa time-of-flight mass detector. MS MS:1003381 ACQUITY RDa Detector Waters Corporation RDa time-of-flight mass detector. PSI:MS Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing. MS MS:1003382 waters_connect Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing. PSI:MS Bruker Daltonics' timsTOF Ultra. MS MS:1003383 timsTOF Ultra Bruker Daltonics' timsTOF Ultra. PSI:MS v?(d+).(d+).(d+)(?:-(S+))? MS MS:1003384 semantic version regexp v?(d+).(d+).(d+)(?:-(S+))? PSI:PI The versioning of the crosslinking mzIdentML extension document. MS MS:1003385 mzIdentML crosslinking extension document version The versioning of the crosslinking mzIdentML extension document. PSI:PI Bioconductor package Spectra for mass spectrometry data representation and processing. MS MS:1003386 Spectra Bioconductor package Spectra for mass spectrometry data representation and processing. PSI:MS https://doi.org/doi:10.18129/B9.bioc.Spectra Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data. MS MS:1003387 MetaboAnnotation Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data. PMID:35208247 PSI:MS https://doi.org/10.3390/metabo12020173 https://doi.org/doi:10.18129/B9.bioc.MetaboAnnotation Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries. MS MS:1003388 CompoundDb Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries. PMID:35208247 PSI:MS https://doi.org/10.3390/metabo12020173 https://doi.org/doi:10.18129/B9.bioc.CompoundDb Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence. MS MS:1003389 mzTab-M Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence. PMID:30688441 PMID:31525911 https://www.psidev.info/mztab Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots <name>:<mass>:<pairs with>. MS MS:1003390 crosslinker cleavage characteristics Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots <name>:<mass>:<pairs with>. PSI:PI ^(?<NAME>[A-Za-z]):(?<MASS>[+-]?[0-9]+(.[0-9]+)?([eE][+-]?[0-9]+(.[0-9]+)?)?):(?<PAIRS_WITH>[A-Za-z]+)$ MS MS:1003391 crosslinker cleavage regular expression ^(?<NAME>[A-Za-z]):(?<MASS>[+-]?[0-9]+(.[0-9]+)?([eE][+-]?[0-9]+(.[0-9]+)?)?):(?<PAIRS_WITH>[A-Za-z]+)$ PSI:PI A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses. MS MS:1003392 search modification id A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses. PSI:PI A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance. MS MS:1003393 search modification id ref A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance. PSI:PI RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF. MS MS:1003394 SelexION separation voltage RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF. PSI:MS Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer. MS MS:1003395 Q Exactive GC Orbitrap Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer. PSI:MS Agilent 8890 Gas Chromatograph System. MS MS:1003396 8890 GC/MS Agilent 8890 Gas Chromatograph System. PSI:MS Bruker Daltonics' timsTOF fleX MALDI-2. MS MS:1003397 timsTOF fleX MALDI-2 Bruker Daltonics' timsTOF fleX MALDI-2. PSI:MS The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file. MS MS:1003398 deconvoluted data The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file. PSI:MS Software that creates or manipulates QC-related data. MS MS:1003399 quality control software Software that creates or manipulates QC-related data. PSI:MS An R package for reading, validating, and writing mzQC files. MS MS:1003400 rmzqc An R package for reading, validating, and writing mzQC files. https://github.com/MS-Quality-hub/rmzqc A Java package for reading, validating, and writing mzQC files. MS MS:1003401 jmzqc A Java package for reading, validating, and writing mzQC files. https://github.com/MS-Quality-hub/jmzqc A Python package for reading, validating, and writing mzQC files. MS MS:1003402 pymzqc A Python package for reading, validating, and writing mzQC files. https://github.com/MS-Quality-hub/pymzqc IUPAC International Chemical Identifier. MS MS:1003403 InChI IUPAC International Chemical Identifier. PMID:26136848 Bruker Daltonics' timsTOF HT. MS MS:1003404 timsTOF HT Bruker Daltonics' timsTOF HT. PSI:MS MS1 recalibration using identified peptides as internal calibrants. MS MS:1003405 mzRecal MS1 recalibration using identified peptides as internal calibrants. DOI:10.1093/bioinformatics/btab056 PMID:33538780 https://github.com/524D/mzrecal Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte. MS MS:1003406 spectrum clustering software Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte. PSI:MS Identifying crosslinked peptides in complex protein mixtures MS MS:1003407 Scout Identifying crosslinked peptides in complex protein mixtures PMID:39482464 Scout identification search engine score MS MS:1003408 Scout score Scout identification search engine score PSI:MS Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer. MS MS:1003409 Stellar Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer. PSI:MS The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD). MS MS:1003410 electron beam energy The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD). PSI:MS Thermo Scientific Orbitrap IQ-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. MS MS:1003411 Orbitrap IQ-X Thermo Scientific Orbitrap IQ-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. PSI:MS Bruker Daltonics timsTOF Ultra 2. MS MS:1003412 timsTOF Ultra 2 Bruker Daltonics timsTOF Ultra 2. PSI:MS Kojak open-source crosslinked peptide sequence search engine developed at the Institute for Systems Biology. MS MS:1003413 Kojak Kojak open-source crosslinked peptide sequence search engine developed at the Institute for Systems Biology. PMID:36629399 The Kojak score for an individual peptide sequence, similar to Comet:xcorr. MS MS:1003414 Kojak:score The Kojak score for an individual peptide sequence, similar to Comet:xcorr. PSI:PI The Kojak expectation value for an individual peptide sequence. MS MS:1003415 Kojak:expectation value The Kojak expectation value for an individual peptide sequence. PSI:PI The number of matched ions for an individual peptide sequence in a Kojak result. MS MS:1003416 Kojak:matched ions The number of matched ions for an individual peptide sequence in a Kojak result. PSI:PI The highest run of consecutive matched ions for an individual peptide sequence in a Kojak result. MS MS:1003417 Kojak:consecutive matched ions The highest run of consecutive matched ions for an individual peptide sequence in a Kojak result. PSI:PI The difference between the top Kojak score and the next best Kojak score for a PSM. MS MS:1003418 Kojak:delta score The difference between the top Kojak score and the next best Kojak score for a PSM. PSI:PI The rank of an individual peptide from the first pass of the Kojak scoring algorithm. Applies only to sequences in a crosslinked result. MS MS:1003419 Kojak:rank The rank of an individual peptide from the first pass of the Kojak scoring algorithm. Applies only to sequences in a crosslinked result. PSI:PI The Kojak score for a crosslinked pair of peptide sequences, similar to Comet:xcorr. MS MS:1003420 Kojak:score xlink The Kojak score for a crosslinked pair of peptide sequences, similar to Comet:xcorr. PSI:PI The Kojak expectation value for a crosslinked pair of peptide sequences. MS MS:1003421 Kojak:expectation value xlink The Kojak expectation value for a crosslinked pair of peptide sequences. PSI:PI The number of matched ions for a crosslinked pair of peptide sequences in a Kojak result. MS MS:1003422 Kojak:matched ions xlink The number of matched ions for a crosslinked pair of peptide sequences in a Kojak result. PSI:PI Orbitrap Exploris GC 240 Mass Spectrometer. MS MS:1003423 Orbitrap Exploris GC 240 Orbitrap Exploris GC 240 Mass Spectrometer. PSI:MS Spectrum for which the peaks are limited to a subset of known product ions that are important for subsequent identification, whose m/z values are corrected to theoretical values, and intensity values are experimentally derived. MS MS:1003424 selected fragment theoretical m/z observed intensity spectrum Spectrum for which the peaks are limited to a subset of known product ions that are important for subsequent identification, whose m/z values are corrected to theoretical values, and intensity values are experimentally derived. PSI:PI Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data. MS MS:1003425 quantms Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data. PMID:38965444 A software to identify cross-linked peptides from LC-MS/MS spectra. MS MS:1003426 xQuest/xProphet A software to identify cross-linked peptides from LC-MS/MS spectra. PMID:18327264 A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data. MS MS:1003427 PeakView A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data. PMID:32275110 A software for interpreting protein quantification, interaction and post-translational modification data. MS MS:1003428 Perseus A software for interpreting protein quantification, interaction and post-translational modification data. PMID:27348712 A computational platform for analyzing mass spectrometry-based proteomics data. MS MS:1003429 FragPipe A computational platform for analyzing mass spectrometry-based proteomics data. PMID:37878603 A software for LC-MS data management and analysis. MS MS:1003430 OpenMS A software for LC-MS data management and analysis. PMID:38366242 A tool for the analysis of chemically cross-linked proteins using mass spectrometry. MS MS:1003431 pLink A tool for the analysis of chemically cross-linked proteins using mass spectrometry. PMID:22772728 Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure. MS MS:1003432 pLink2 Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure. PMID:31363125 Score difference to the second best identified peptide with a different amino acid sequence. MS MS:1003433 Andromeda:delta score Score difference to the second best identified peptide with a different amino acid sequence. PSI:PI A serine protease that hydrolyzes peptide bonds at the C-terminus of threonine, alanine, serine, and valine. (EC:3.4.21.12) alpha-lytic endopeptidase alpha-lytic protease MS MS:1003434 AlphaLP A serine protease that hydrolyzes peptide bonds at the C-terminus of threonine, alanine, serine, and valine. (EC:3.4.21.12) DOI:10.1021/bi00445a015 DOI:10.1038/228438a0 Regular expression for alphaLP. MS MS:1003435 (?<=[TSAV]) Regular expression for alphaLP. PSI:PI PSI Quality Control controlled vocabulary term. MS MS:4000000 PSI-MS CV Quality Control Vocabulary PSI Quality Control controlled vocabulary term. PSI:MS Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations. MS MS:4000001 QC metric Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations. PSI:MS The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix. MS MS:4000002 QC metric value type The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix. PSI:MS Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). MS MS:4000003 single value Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). PSI:MS Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable). MS MS:4000004 n-tuple Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable). PSI:MS Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). MS MS:4000005 The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns. table Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). PSI:MS A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable). MS MS:4000006 The actual structure of the matrix is defined in the mzQC specification document. matrix A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable). PSI:MS Categorization of the QC metric. MS MS:4000007 QC metric category Categorization of the QC metric. PSI:MS QC metric based on identification results. MS MS:4000008 ID based metric QC metric based on identification results. PSI:MS QC metric not based on identification results. MS MS:4000009 ID free metric QC metric not based on identification results. PSI:MS QC metric based on quantification results. MS MS:4000010 quantification based metric QC metric based on quantification results. PSI:MS QC metric calculated from a single run (e.g. one .raw file). MS MS:4000012 single run based metric QC metric calculated from a single run (e.g. one .raw file). PSI:MS QC metric calculated from multiple runs (e.g. multiple .raw files). MS MS:4000013 multiple runs based metric QC metric calculated from multiple runs (e.g. multiple .raw files). PSI:MS QC metric calculated from a single spectrum. MS MS:4000014 single spectrum based metric QC metric calculated from a single spectrum. PSI:MS QC metric calculated from multiple spectra. MS MS:4000015 multiple spectra based metric QC metric calculated from multiple spectra. PSI:MS QC metric related to retention time. MS MS:4000016 retention time metric QC metric related to retention time. PSI:MS QC metric related to a chromatogram. MS MS:4000017 chromatogram metric QC metric related to a chromatogram. PSI:MS QC metric related to an extracted ion chromatogram. MS MS:4000018 XIC metric QC metric related to an extracted ion chromatogram. PSI:MS QC metric related to the mass spectrometry acquisition. MS MS:4000019 MS metric QC metric related to the mass spectrometry acquisition. PSI:MS QC metric related to events in the ion source. MS MS:4000020 ion source metric QC metric related to events in the ion source. PSI:MS QC metric based on MS1 events. MS MS:4000021 MS1 metric QC metric based on MS1 events. PSI:MS QC metric based on MS2 events. MS MS:4000022 MS2 metric QC metric based on MS2 events. PSI:MS QC metric related to the sample preparation. MS MS:4000023 sample preparation metric QC metric related to the sample preparation. PSI:MS QC metric related to measurements of the ambient environment, such as the laboratory. MS MS:4000024 environment metric QC metric related to measurements of the ambient environment, such as the laboratory. PSI:MS Representation of the ion current assigned to detected precursors in the series of all MS1 spectra versus time. precursor ion chromatogram MS MS:4000025 precursor ion current chromatogram Representation of the ion current assigned to detected precursors in the series of all MS1 spectra versus time. PSI:MS The median of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied. MS MS:4000026 Factors like temperature, airflow, or instrument calibration can cause mass shifts. fragment ppm deviation median The median of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied. PSI:MS The mean of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied MS MS:4000027 Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000178 for the MS1 equivalent. fragment ppm deviation mean The mean of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied PSI:MS The standard deviation of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied MS MS:4000028 Factors like temperature, airflow, or instrument calibration can cause mass shifts. See MS:4000179 for the MS1 equivalent. fragment ppm deviation sigma The standard deviation of the distribution of observed fragment mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied PSI:MS The area under the total ion current chromatogram (MS:1000235) of all MS1 spectra. MS MS:4000029 The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. The signal can be affected by contamination, retention time shifts, or loss of hydrophilic/hydrophobic peptides. area under TIC in MS1 The area under the total ion current chromatogram (MS:1000235) of all MS1 spectra. PSI:MS The area under the total ion current chromatogram (MS:1000235) of all MS2 spectra. MS MS:4000030 The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. The signal can be affected by contamination, retention time shifts, or loss of hydrophilic/hydrophobic peptides. Issues such as contamination on the MS front-end and fragmentation efficiency can lead to poor MS signals. Contamination would decrease both MS1 and MS2 S/N, while poor fragmentation efficiency affects MS2 signal but leaves MS1 signal unchanged. area under TIC in MS2 The area under the total ion current chromatogram (MS:1000235) of all MS2 spectra. PSI:MS The ratio of the area under TIC of MS1 (MS:4000029) divided by the area under the TIC of MS2 (MS:4000030). MS MS:4000031 Poor fragmentation efficiency or precursor fragmentation intensity thresholds affect MS2 signal but leave MS1 signal unchanged. peak area of MS1 vs MS2 signal ratio The ratio of the area under TIC of MS1 (MS:4000029) divided by the area under the TIC of MS2 (MS:4000030). PSI:MS The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC. XIC-WideFrac MS MS:4000050 This metric characterises the distribution of precursor peak widths, much as the N50 characterises contig sizes in genome assembly. XIC50 fraction The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC. PSI:MS XIC-WideFrac PMID:24494671 The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3. MS XIC-FWHM-Q1 XIC-FWHM-Q2 XIC-FWHM-Q3 MS:4000051 XIC-FWHM quantiles The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3. PSI:MS XIC-FWHM-Q1 PMID:24494671 XIC-FWHM-Q2 PMID:24494671 XIC-FWHM-Q3 PMID:24494671 OBSOLETE. The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. MS:4000182 MS XIC-Height-Q2 XIC-Height-Q3 XIC-Height-Q4 MS:4000052 obsolete XIC-Height quartile ratios true OBSOLETE. The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. PSI:MS XIC-Height-Q2 PMID:24494671 XIC-Height-Q3 PMID:24494671 XIC-Height-Q4 PMID:24494671 The retention time duration of the chromatography in seconds. MS RT-Duration MS:4000053 Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. chromatography duration The retention time duration of the chromatography in seconds. PSI:MS RT-Duration PMID:24494671 OBSOLETE. The interval when the respective quarter of the TIC accumulates divided by retention time duration. MS:4000183 MS RT-TIC-Q1 RT-TIC-Q2 RT-TIC-Q3 RT-TIC-Q4 MS:4000054 The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run. obsolete TIC quarters RT fraction true OBSOLETE. The interval when the respective quarter of the TIC accumulates divided by retention time duration. PSI:MS RT-TIC-Q1 PMID:24494671 RT-TIC-Q2 PMID:24494671 RT-TIC-Q3 PMID:24494671 RT-TIC-Q4 PMID:24494671 OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. MS:4000184 MS RT-MS-Q1 RT-MS-Q2 RT-MS-Q3 RT-MS-Q4 MS:4000055 The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type. obsolete MS1 quarter RT fraction true OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. PSI:MS RT-MS-Q1 PMID:24494671 RT-MS-Q2 PMID:24494671 RT-MS-Q3 PMID:24494671 RT-MS-Q4 PMID:24494671 OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. MS:4000185 MS RT-MSMS-Q1 RT-MSMS-Q2 RT-MSMS-Q3 RT-MSMS-Q4 MS:4000056 The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. obsolete MS2 quarter RT fraction true OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. PSI:MS RT-MSMS-Q1 PMID:24494671 RT-MSMS-Q2 PMID:24494671 RT-MSMS-Q3 PMID:24494671 RT-MSMS-Q4 PMID:24494671 OBSOLETE. The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 MS:4000186 MS MS1-TIC-Change-Q2 MS1-TIC-Change-Q3 MS1-TIC-Change-Q4 MS:4000057 The metric informs about the dynamic range of the acquisition along the chromatographic separation.This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant. obsolete MS1 TIC-change quartile ratios true OBSOLETE. The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 PSI:MS MS1-TIC-Change-Q2 PMID:24494671 MS1-TIC-Change-Q3 PMID:24494671 MS1-TIC-Change-Q4 PMID:24494671 OBSOLETE. The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. MS:4000187 MS MS1-TIC-Q2 MS1-TIC-Q3 MS1-TIC-Q4 MS:4000058 The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples. obsolete MS1 TIC quartile ratios true OBSOLETE. The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. PSI:MS MS1-TIC-Q2 PMID:24494671 MS1-TIC-Q3 PMID:24494671 MS1-TIC-Q4 PMID:24494671 The number of MS1 events in the run. MS1-Count MS MS:4000059 An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. number of MS1 spectra The number of MS1 events in the run. PSI:MS MS1-Count PMID:24494671 The number of MS2 events in the run. MS2-Count MS MS:4000060 An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. number of MS2 spectra The number of MS2 events in the run. PSI:MS MS2-Count PMID:24494671 The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode. MS1 peak density distribution - quantiles MS MS1-Density-Q1 MS1-Density-Q2 MS1-Density-Q3 MS:4000061 MS1 density quantiles The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode. PSI:MS MS1-Density-Q1 PMID:24494671 MS1-Density-Q2 PMID:24494671 MS1-Density-Q3 PMID:24494671 The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode. MS2 peak density distribution - quantiles MS MS2-Density-Q1 MS2-Density-Q2 MS2-Density-Q3 MS:4000062 MS2 density quantiles The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode. PSI:MS MS2-Density-Q1 PMID:24494671 MS2-Density-Q2 PMID:24494671 MS2-Density-Q3 PMID:24494671 The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher. MS2-PrecZ-1 MS2-PrecZ-2 MS2-PrecZ-3 MS2-PrecZ-4 MS2-PrecZ-5 MS2-PrecZ-more MS IS-3A IS-3B IS-3C MS:4000063 the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2. MS2 known precursor charges fractions The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher. PSI:MS MS2-PrecZ-1 PMID:24494671 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-3 PMID:24494671 MS2-PrecZ-4 PMID:24494671 MS2-PrecZ-5 PMID:24494671 MS2-PrecZ-more PMID:24494671 IS-3A PMID:19837981 IS-3B PMID:19837981 IS-3C PMID:19837981 The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states. MS MS2-PrecZ-likely-1 MS2-PrecZ-likely-multi MS:4000064 MS2 unknown and likely precursor charges fractions The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states. PSI:MS MS2-PrecZ-likely-1 PMID:24494671 MS2-PrecZ-likely-multi PMID:24494671 Fastest frequency for MS level 1 collection MS1-Freq-Max MS MS:4000065 Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. fastest frequency for MS level 1 collection Fastest frequency for MS level 1 collection PSI:MS MS1-Freq-Max PMID:24494671 Fastest frequency for MS level 2 collection MS2-Freq-Max MS MS:4000066 Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. fastest frequency for MS level 2 collection Fastest frequency for MS level 2 collection PSI:MS MS2-Freq-Max PMID:24494671 The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds. MS MS:4000067 MS run duration The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds. PSI:MS The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well. MS MS:4000068 spectra half-TIC The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well. PSI:MS Upper and lower limit of m/z precursor values at which MSn spectra are recorded. MS MS:4000069 The metric informs about the dynamic range of the acquisition. Based on the used MS instrument configuration, the values should be similar. Variations between measurements may arise when employing acquisition in DDA mode. m/z acquisition range Upper and lower limit of m/z precursor values at which MSn spectra are recorded. PSI:MS Upper and lower limit of retention time at which spectra are recorded. MS MS:4000070 An unusual low range may indicate incomplete sampling and/or a premature or failed LC run. retention time acquisition range Upper and lower limit of retention time at which spectra are recorded. PSI:MS The number of chromatograms recorded for the run. MS MS:4000071 number of chromatograms The number of chromatograms recorded for the run. PSI:MS Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum. MS MS:4000072 observed mass accuracy Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum. PSI:MS A QC metric based on a QC sample of known content. MS MS:4000073 QC sample metric A QC metric based on a QC sample of known content. PSI:MS A QC metric based on a QC sample of known and high complexity content. MS MS:4000074 high complexity QC sample metric A QC metric based on a QC sample of known and high complexity content. PSI:MS A QC metric based on a QC sample of known and low complexity content. MS MS:4000075 low complexity QC sample metric A QC metric based on a QC sample of known and low complexity content. PSI:MS A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design. MS MS:4000076 Expected peptides from QC2 sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR' QC2 sample metric A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design. PMID:23088386 PMID:29324744 PSI:MS A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design). MS MS:4000077 Expected peptides from QC1 sample measurement are: 'LVNELTEFAK','HLVDEPQNLIK','VPQVSTPTLVEVSR','EAC(Carbamidomethyl)FAVEGPK','EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK','EC(Carbamidomethyl)C(Carbamidomethyl)HGDLLEC(Carbamidomethyl)ADDR','SLHTLFGDELC(Carbamidomethyl)K','TC(Carbamidomethyl)VADESHAGC(Carbamidomethyl)EK','YIC(Carbamidomethyl)DNQDTISSK','NEC(Carbamidomethyl)FLSHK' QC1 sample metric A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design). PMID:23088386 PMID:29324744 PSI:MS Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected. MS MS:4000078 QC2 sample mass accuracies Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected. PSI:MS Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected. MS MS:4000079 QC2 sample intensities Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected. PSI:MS QC terms associated but not directly metrics themselves. MS MS:4000080 QC non-metric term QC terms associated but not directly metrics themselves. PSI:MS Data from the first principal component of a PCA. 1st PC MS MS:4000081 first principal component Data from the first principal component of a PCA. PSI:MS Data from the second principal component of a PCA. 2nd PC MS MS:4000082 second principal component Data from the second principal component of a PCA. PSI:MS Data from the third principal component of a PCA. 3rd PC MS MS:4000083 third principal component Data from the third principal component of a PCA. PSI:MS Data from the fourth principal component of a PCA. 4th PC MS MS:4000084 fourth principal component Data from the fourth principal component of a PCA. PSI:MS Data from the fifth principal component of a PCA. 5th PC MS MS:4000085 fifth principal component Data from the fifth principal component of a PCA. PSI:MS Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels. MS MS:4000086 mzQC input reference Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels. PSI:MS Used to supply alternative labels for plotting figures. MS MS:4000087 mzQC plot label Used to supply alternative labels for plotting figures. PSI:MS Used to supply batch label information with any string value. MS MS:4000088 batch label Used to supply batch label information with any string value. PSI:MS Used to supply injection sequence information with consecutive whole numbers. MS MS:4000089 injection sequence label Used to supply injection sequence information with consecutive whole numbers. PSI:MS A table with the PCA results of MaxQuant's protein group raw intensities. MS MS:4000090 principal component analysis of MaxQuant's protein group raw intensities A table with the PCA results of MaxQuant's protein group raw intensities. maxquant:table:directory&s[]=output PSI:MS A table with the PCA results of MaxQuant's protein group lfq intensities. MS MS:4000091 principal component analysis of MaxQuant's protein group lfq intensities A table with the PCA results of MaxQuant's protein group lfq intensities. maxquant:table:directory&s[]=output PSI:MS A table with the PCA results of identified MS1 feature areas. MS MS:4000092 identified MS1 feature area principal component analysis result A table with the PCA results of identified MS1 feature areas. PSI:MS A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas. MS MS:4000093 unidentified MS1 feature area principal component analysis result A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas. PSI:MS A table with the PCA results of identified MS1 feature areas after batch-correction. MS MS:4000094 batch-corrected identified MS1 feature area principal component analysis result A table with the PCA results of identified MS1 feature areas after batch-correction. PSI:MS The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. MS MS:4000095 slowest frequency for MS level 1 collection The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. PSI:MS The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. MS MS:4000096 slowest frequency for MS level 2 collection The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. PSI:MS The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. MS IS-1A MS:4000097 An unusual high count of signal jumps or falls may indicate ESI stability issues. MS1 signal jump (10x) count The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. PSI:MS The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. MS IS-1B MS:4000098 An unusual high count of signal jumps or falls may indicate ESI stability issues. MS1 signal fall (10x) count The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. PSI:MS Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). MS MS:4000099 An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. number of empty MS1 scans Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). PSI:MS Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). MS MS:4000100 An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. number of empty MS2 scans Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). PSI:MS Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). MS MS:4000101 An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. number of empty MS3 scans Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). PSI:MS The number of data points detected for quantification purposes within the run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. MS MS:4000102 number of detected quantification data points The number of data points detected for quantification purposes within the run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. PSI:MS The number of identified data points for quantification purposes within the run after user defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000103 number of identified quantification data points The number of identified data points for quantification purposes within the run after user defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS Tabular representation of the total ion current detected in each of a series of mass spectra. MS MS:4000104 total ion currents Tabular representation of the total ion current detected in each of a series of mass spectra. PSI:MS Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition. MS MS:4000105 ion injection parameters Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition. PSI:MS Average MS1 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.) MS MS:4000106 Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content. MS1 frequency in equal parts of subsequent RT Average MS1 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.) PSI:MS Average MS2 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.) MS MS:4000107 Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content. MS2 frequency in equal parts of subsequent RT Average MS2 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.) PSI:MS From the distribution of peak densities in MS1, the mean MS MS:4000108 The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. MS1 peak density distribution mean From the distribution of peak densities in MS1, the mean PSI:MS From the distribution of peak densities in MS1, the sigma value MS MS:4000109 The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. MS1 peak density distribution sigma From the distribution of peak densities in MS1, the sigma value PSI:MS From the distribution of peak densities in MS1, the list of outliers below a in-file defined threshold MS MS:4000110 The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. MS1 peak density distribution low outliers From the distribution of peak densities in MS1, the list of outliers below a in-file defined threshold PSI:MS From the distribution of peak densities in MS1, the list of outliers above a in-file defined threshold MS MS:4000111 The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. MS1 peak density distribution high outliers From the distribution of peak densities in MS1, the list of outliers above a in-file defined threshold PSI:MS From the distribution of peak densities in MS2, the mean MS MS:4000112 The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. MS2 peak density distribution mean From the distribution of peak densities in MS2, the mean PSI:MS From the distribution of peak densities in MS2, the sigma value MS MS:4000113 The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. MS2 peak density distribution sigma From the distribution of peak densities in MS2, the sigma value PSI:MS From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold MS MS:4000114 The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. MS2 peak density distribution low outliers From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold PSI:MS From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold MS MS:4000115 The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. MS2 peak density distribution high outliers From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold PSI:MS From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. MS MS:4000116 The intensity distribution of the precursors informs about the dynamic range of the acquisition. MS2 precursor intensity distribution From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. PSI:MS From the distribution of MS2 precursor intensities, the mean MS MS:4000117 The intensity distribution of the precursors informs about the dynamic range of the acquisition. MS2 precursor intensity distribution mean From the distribution of MS2 precursor intensities, the mean PSI:MS From the distribution of MS2 precursor intensities, the sigma value MS MS:4000118 The intensity distribution of the precursors informs about the dynamic range of the acquisition. MS2 precursor intensity distribution sigma From the distribution of MS2 precursor intensities, the sigma value PSI:MS From the distribution of precursor intensities, the list of outliers below a in-file defined threshold MS MS:4000119 The intensity distribution of the precursors informs about the dynamic range of the acquisition. MS2 precursor intensity distribution low outliers From the distribution of precursor intensities, the list of outliers below a in-file defined threshold PSI:MS From the distribution of precursor intensities, the list of outliers above a in-file defined threshold MS MS:4000120 The intensity distribution of the precursors informs about the dynamic range of the acquisition. MS2 precursor intensity distribution high outliers From the distribution of precursor intensities, the list of outliers above a in-file defined threshold PSI:MS From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 MS MS:4000121 The Signal-to-noise ratio in MS1 distribution can provide insight to the presence of nuisance factors. MS1 signal-to-noise ratio quantiles From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 PSI:MS From the distribution of signal-to-noise ratio in MS1, the mean MS MS:4000122 The signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS1 signal-to-noise ratio mean From the distribution of signal-to-noise ratio in MS1, the mean PSI:MS From the distribution of signal-to-noise ratio in MS1, the sigma value MS MS:4000123 The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS1 signal-to-noise ratio sigma From the distribution of signal-to-noise ratio in MS1, the sigma value PSI:MS From the distribution of signal-to-noise ratio in MS1, the list of outliers below a in-file defined threshold MS MS:4000124 The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS1 signal-to-noise ratio low outliers From the distribution of signal-to-noise ratio in MS1, the list of outliers below a in-file defined threshold PSI:MS From the distribution of signal-to-noise ratio in MS1, the list of outliers above a in-file defined threshold MS MS:4000125 The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS1 signal-to-noise ratio high outliers From the distribution of signal-to-noise ratio in MS1, the list of outliers above a in-file defined threshold PSI:MS From the distribution of signal-to-noise ratio in MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 MS MS:4000126 A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS2 signal-to-noise ratio quantiles From the distribution of signal-to-noise ratio in MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 PSI:MS From the distribution of signal-to-noise ratio in MS2, the mean MS MS:4000127 A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS2 signal-to-noise ratio mean From the distribution of signal-to-noise ratio in MS2, the mean PSI:MS From the distribution of signal-to-noise ratio in MS2, the sigma value MS MS:4000128 A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS2 signal-to-noise ratio sigma From the distribution of signal-to-noise ratio in MS2, the sigma value PSI:MS From the distribution of signal-to-noise ratio in MS2, the list of outliers below a in-file defined threshold MS MS:4000129 A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS2 signal-to-noise ratio low outliers From the distribution of signal-to-noise ratio in MS2, the list of outliers below a in-file defined threshold PSI:MS From the distribution of signal-to-noise ratio in MS2, the list of outliers above a in-file defined threshold MS MS:4000130 A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). MS2 signal-to-noise ratio high outliers From the distribution of signal-to-noise ratio in MS2, the list of outliers above a in-file defined threshold PSI:MS From the distribution of ion injection times (MS:1000927) for MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 MS MS:4000131 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS1 ion collection time quantiles From the distribution of ion injection times (MS:1000927) for MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 PSI:MS From the distribution of ion injection times (MS:1000927) for MS1, the mean MS MS:4000132 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS1 ion collection time mean From the distribution of ion injection times (MS:1000927) for MS1, the mean PSI:MS From the distribution of ion injection times (MS:1000927) for MS1, the sigma value MS MS:4000133 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS1 ion collection time sigma From the distribution of ion injection times (MS:1000927) for MS1, the sigma value PSI:MS From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below a in-file defined threshold MS MS:4000134 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS1 ion collection time low outliers From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below a in-file defined threshold PSI:MS From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above a in-file defined threshold MS MS:4000135 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS1 ion collection time high outliers From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above a in-file defined threshold PSI:MS From the distribution of ion injection times (MS:1000927) for MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 MS MS:4000136 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS2 ion collection time quantiles From the distribution of ion injection times (MS:1000927) for MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 PSI:MS From the distribution of ion injection times (MS:1000927) for MS2, the mean MS MS:4000137 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS2 ion collection time mean From the distribution of ion injection times (MS:1000927) for MS2, the mean PSI:MS From the distribution of ion injection times (MS:1000927) for MS2, the sigma value MS MS:4000138 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS2 ion collection time sigma From the distribution of ion injection times (MS:1000927) for MS2, the sigma value PSI:MS From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold MS MS:4000139 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS2 ion collection time low outliers From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold PSI:MS From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold MS MS:4000140 Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. MS2 ion collection time high outliers From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold PSI:MS The definition of the outlier criteria applied. MS MS:4000141 outlier threshold criterion The definition of the outlier criteria applied. PSI:MS Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. MS MS:4000142 Tukey's fence Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. PSI:MS Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. MS MS:4000143 Tukey's fence high outliers Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. PSI:MS Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5. MS MS:4000144 Tukey's fence low outliers Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5. PSI:MS Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. MS MS:4000145 Z-score threshold Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. PSI:MS Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. MS MS:4000146 Z-score threshold high outliers Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. PSI:MS Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. MS MS:4000147 Z-score threshold low outliers Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. PSI:MS Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used. MS MS:4000148 algorithmical threshold Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used. PSI:MS A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc. MS MS:4000149 iRT calibration formula A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc. PSI:MS The goodness of fit statistic between observed retention times and iRT calibrated retention times. MS MS:4000150 iRT calibration adjusted r-squared The goodness of fit statistic between observed retention times and iRT calibrated retention times. PSI:MS MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. MS MS:4000151 MsQuality MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. DOI:10.1101/2023.05.12.540477 https://github.com/tnaake/MsQuality/ Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000152 The m/z distribution informs about the dynamic range of the acquisition. MS2 precursor median m/z of identified quantification data points Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS C-2A MS:4000153 Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. interquartile RT period for identified quantification data points The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS C-2A PMID:19837981 The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS C-2B MS:4000154 Higher rates may indicate a more efficient sampling and identification. rate of the interquartile RT period for identified quantification data points The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS C-2B PMID:19837981 The area under the total ion chromatogram. MS MS:4000155 The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. area under TIC The area under the total ion chromatogram. PSI:MS The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple. MS MS:4000156 The metric informs about the dynamic range of the acquisition along the chromatographic separation. Differences between samples of an experiment may indicate differences in chromatographic performance, differences in the dynamic range and/or in the sample content. area under TIC RT quantiles The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple. PSI:MS Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS1-3A MS:4000157 The metric informs about the dynamic range of the acquisition. extent of identified MS2 precursor intensity Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS MS1-3A PMID:19837981 Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000158 The metric informs about the dynamic range of the acquisition along the chromatographic separation. median of TIC values in the RT range in which the middle half of quantification data points are identified Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS1-2B MS:4000159 The metric informs about the dynamic range of the acquisition along the chromatographic separation. median of TIC values in the shortest RT range in which half of the quantification data points are identified Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS MS1-2B PMID:19837981 Minimum and maximum MS2 precursor intensity recorded. MS MS:4000160 The metric informs about the dynamic range of the acquisition. MS2 precursor intensity range Minimum and maximum MS2 precursor intensity recorded. PSI:MS From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000161 The metric informs about the dynamic range of the acquisition in relation to identifiability. identified MS2 precursor intensity distribution From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000162 The metric informs about the dynamic range of the acquisition in relation to identifiability. unidentified MS2 precursor intensity distribution From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000163 The metric informs about the dynamic range of the acquisition in relation to identifiability. identified MS2 precursor intensity distribution mean From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000164 The metric informs about the dynamic range of the acquisition in relation to identifiability. unidentified MS2 precursor intensity distribution mean From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000165 The metric informs about the dynamic range of the acquisition in relation to identifiability. identified MS2 precursor intensity distribution sigma From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS:4000166 The metric informs about the dynamic range of the acquisition in relation to identifiability. unidentified MS2 precursor intensity distribution sigma From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS The ratio of 1+ over 2+ MS2 precursor charge count of all spectra. MS IS-3A MS2 known precursor charges fractions MS2-PrecZ-1 MS2-PrecZ-2 MS:4000167 High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization. ratio of 1+ over 2+ of all MS2 known precursor charges The ratio of 1+ over 2+ MS2 precursor charge count of all spectra. PSI:MS IS-3A PMID:19837981 MS2-PrecZ-1 PMID:24494671 MS2-PrecZ-2 PMID:24494671 The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS IS-3A MS2 known precursor charges fractions MS2-PrecZ-1 MS2-PrecZ-2 MS:4000168 High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization in relation to identifiability. ratio of 1+ over 2+ of identified MS2 known precursor charges The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS IS-3A PMID:19837981 MS2-PrecZ-1 PMID:24494671 MS2-PrecZ-2 PMID:24494671 The ratio of 3+ over 2+ MS2 precursor charge count of all spectra. MS IS-3B MS2 known precursor charges fractions MS2-PrecZ-2 MS2-PrecZ-3 MS:4000169 Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. ratio of 3+ over 2+ of all MS2 known precursor charges The ratio of 3+ over 2+ MS2 precursor charge count of all spectra. PSI:MS IS-3B PMID:19837981 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-3 PMID:24494671 The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS IS-3B MS2 known precursor charges fractions MS2-PrecZ-2 MS2-PrecZ-3 MS:4000170 Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. ratio of 3+ over 2+ of identified MS2 known precursor charges The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS IS-3B PMID:19837981 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-3 PMID:24494671 The ratio of 4+ over 2+ MS2 precursor charge count of all spectra. MS IS-3C MS2 known precursor charges fractions MS2-PrecZ-2 MS2-PrecZ-4 MS:4000171 Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. ratio of 4+ over 2+ of all MS2 known precursor charges The ratio of 4+ over 2+ MS2 precursor charge count of all spectra. PSI:MS IS-3C PMID:19837981 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-4 PMID:24494671 The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS IS-3C MS2 known precursor charges fractions MS2-PrecZ-2 MS2-PrecZ-4 MS:4000172 Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. ratio of 4+ over 2+ of identified MS2 known precursor charges The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS IS-3C PMID:19837981 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-4 PMID:24494671 Mean MS2 precursor charge in all spectra MS MS2 known precursor charges fractions MS2-PrecZ-1 MS2-PrecZ-2 MS2-PrecZ-3 MS2-PrecZ-4 MS2-PrecZ-5 MS2-PrecZ-more MS:4000173 Higher charges may indicate inefficient ionization or e.g. preference for longer peptides. mean MS2 precursor charge in all spectra Mean MS2 precursor charge in all spectra PSI:MS MS2-PrecZ-1 PMID:24494671 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-3 PMID:24494671 MS2-PrecZ-4 PMID:24494671 MS2-PrecZ-5 PMID:24494671 MS2-PrecZ-more PMID:24494671 Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS2 known precursor charges fractions MS2-PrecZ-1 MS2-PrecZ-2 MS2-PrecZ-3 MS2-PrecZ-4 MS2-PrecZ-5 MS2-PrecZ-more MS:4000174 Higher charges may indicate inefficient ionization or e.g. preference for longer peptides in relation to identifiability. mean MS2 precursor charge in identified spectra Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS MS2-PrecZ-1 PMID:24494671 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-3 PMID:24494671 MS2-PrecZ-4 PMID:24494671 MS2-PrecZ-5 PMID:24494671 MS2-PrecZ-more PMID:24494671 Median MS2 precursor charge in all spectra MS MS2 known precursor charges fractions MS2-PrecZ-1 MS2-PrecZ-2 MS2-PrecZ-3 MS2-PrecZ-4 MS2-PrecZ-5 MS2-PrecZ-more MS:4000175 Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides. median MS2 precursor charge in all spectra Median MS2 precursor charge in all spectra PSI:MS MS2-PrecZ-1 PMID:24494671 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-3 PMID:24494671 MS2-PrecZ-4 PMID:24494671 MS2-PrecZ-5 PMID:24494671 MS2-PrecZ-more PMID:24494671 Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS MS2 known precursor charges fractions MS2-PrecZ-1 MS2-PrecZ-2 MS2-PrecZ-3 MS2-PrecZ-4 MS2-PrecZ-5 MS2-PrecZ-more MS:4000176 Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides in relation to identifiability. median MS2 precursor charge in identified spectra Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS MS2-PrecZ-1 PMID:24494671 MS2-PrecZ-2 PMID:24494671 MS2-PrecZ-3 PMID:24494671 MS2-PrecZ-4 PMID:24494671 MS2-PrecZ-5 PMID:24494671 MS2-PrecZ-more PMID:24494671 The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database). PG: Contaminants MS MS:4000177 "High values may indicate a sample handling issue, and/or insufficient sample concentration." contaminant protein abundance fraction The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database). PSI:MS The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied MS MS:4000178 precursor ppm deviation mean The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied PSI:MS The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied MS MS:4000179 precursor ppm deviation sigma The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied PSI:MS The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher. MS MS:4000180 table of missed cleavage counts The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher. PSI:MS OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. MS:4000188 MS RT-MSMS-Q1 RT-MSMS-Q2 RT-MSMS-Q3 RT-MSMS-Q4 MS:4000181 The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. obsolete identified MS2 quarter RT fraction true OBSOLETE. The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. PSI:MS RT-MSMS-Q1 PMID:24494671 RT-MSMS-Q2 PMID:24494671 RT-MSMS-Q3 PMID:24494671 RT-MSMS-Q4 PMID:24494671 The log ratio of successive XIC height quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of XIC-Height-Q2 to XIC-Height-Q1, XIC-Height-Q3 to XIC-Height-Q2, XIC-Height max to XIC-Height-Q3. The number of values in the tuple implies the quantile mode. MS XIC-Height-Q2 XIC-Height-Q3 XIC-Height-Q4 MS:4000182 XIC-Height quantile ratios The log ratio of successive XIC height quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of XIC-Height-Q2 to XIC-Height-Q1, XIC-Height-Q3 to XIC-Height-Q2, XIC-Height max to XIC-Height-Q3. The number of values in the tuple implies the quantile mode. PSI:MS XIC-Height-Q2 PMID:24494671 XIC-Height-Q3 PMID:24494671 XIC-Height-Q4 PMID:24494671 The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of values in the tuple implies the quantile mode. MS RT-TIC-Q1 RT-TIC-Q2 RT-TIC-Q3 RT-TIC-Q4 MS:4000183 The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run. TIC quantile RT fraction The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of values in the tuple implies the quantile mode. PSI:MS RT-TIC-Q1 PMID:24494671 RT-TIC-Q2 PMID:24494671 RT-TIC-Q3 PMID:24494671 RT-TIC-Q4 PMID:24494671 The interval used for acquisition of quantiles of all MS1 events divided by retention time duration. The number of values in the tuple implies the quantile mode. MS RT-MS-Q1 RT-MS-Q2 RT-MS-Q3 RT-MS-Q4 MS:4000184 The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type. MS1 quantile RT fraction The interval used for acquisition of quantiles of all MS1 events divided by retention time duration. The number of values in the tuple implies the quantile mode. PSI:MS RT-MS-Q1 PMID:24494671 RT-MS-Q2 PMID:24494671 RT-MS-Q3 PMID:24494671 RT-MS-Q4 PMID:24494671 The interval used for acquisition of quantiles of all MS2 events divided by retention time duration. The number of values in the tuple implies the quantile mode. MS RT-MSMS-Q1 RT-MSMS-Q2 RT-MSMS-Q3 RT-MSMS-Q4 MS:4000185 The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. MS2 quantile RT fraction The interval used for acquisition of quantiles of all MS2 events divided by retention time duration. The number of values in the tuple implies the quantile mode. PSI:MS RT-MSMS-Q1 PMID:24494671 RT-MSMS-Q2 PMID:24494671 RT-MSMS-Q3 PMID:24494671 RT-MSMS-Q4 PMID:24494671 The log ratios of successive TIC-change quantiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. A value triplet represents the original QuaMeter metrics, the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3. The number of values in the tuple implies the quantile mode. MS MS1-TIC-Change-Q2 MS1-TIC-Change-Q3 MS1-TIC-Change-Q4 MS:4000186 The metric informs about the dynamic range of the acquisition along the chromatographic separation. This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant. MS1 TIC-change quantile ratios The log ratios of successive TIC-change quantiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. A value triplet represents the original QuaMeter metrics, the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3. The number of values in the tuple implies the quantile mode. PSI:MS MS1-TIC-Change-Q2 PMID:24494671 MS1-TIC-Change-Q3 PMID:24494671 MS1-TIC-Change-Q4 PMID:24494671 The log ratios of successive TIC quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. The number of values in the tuple implies the quantile mode. MS MS1-TIC-Q2 MS1-TIC-Q3 MS1-TIC-Q4 MS:4000187 The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples. MS1 TIC quantile ratios The log ratios of successive TIC quantiles. A value triplet represents the original QuaMeter metrics, the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. The number of values in the tuple implies the quantile mode. PSI:MS MS1-TIC-Q2 PMID:24494671 MS1-TIC-Q3 PMID:24494671 MS1-TIC-Q4 PMID:24494671 The interval used for acquisition of quantiles of all identified MS2 events, after user-defined acceptance criteria are applied, divided by retention time duration. The number of values in the tuple implies the quantile mode. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. MS RT-MSMS-Q1 RT-MSMS-Q2 RT-MSMS-Q3 RT-MSMS-Q4 MS:4000188 The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. identified MS2 quantile RT fraction The interval used for acquisition of quantiles of all identified MS2 events, after user-defined acceptance criteria are applied, divided by retention time duration. The number of values in the tuple implies the quantile mode. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. PSI:MS RT-MSMS-Q1 PMID:24494671 RT-MSMS-Q2 PMID:24494671 RT-MSMS-Q3 PMID:24494671 RT-MSMS-Q4 PMID:24494671 The number of times something happened. Number of Occurrences MS NCIT:C150827 Number of Occurrences The number of times something happened. NCI Number of Occurrences PT NCI An organizational header for concepts representing mostly abstract entities. Conceptual Entity MS NCIT:C20181 Conceptual Entity An organizational header for concepts representing mostly abstract entities. NCI Conceptual Entity PT NCI A distinguishing quality or prominent aspect of a person, object, action, process, or substance. Property or Attribute MS NCIT:C20189 Property or Attribute A distinguishing quality or prominent aspect of a person, object, action, process, or substance. NCI Property or Attribute PT NCI Property or Attribute PT NICHD Terms used to indicate units of time or other terms associated with time. Temporal Qualifier MS NCIT:C21514 Temporal Qualifier Terms used to indicate units of time or other terms associated with time. NCI Temporal Qualifier PT NCI Temporal Qualifier PT NICHD The period of time during which something continues. MS NCIT:C25330 Duration The period of time during which something continues. NCI A numeral or string of numerals expressing value, quantity, or identification. MS NCIT:C25337 Number A numeral or string of numerals expressing value, quantity, or identification. NCI A thing done. Action Generic Action MS NCIT:C25404 Action A thing done. NCI Action PT NCI Action SY caDSR Generic Action SY NCI The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. Characteristic Characteristics Feature Features MS NCIT:C25447 Characteristic The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. NCI Characteristic PT NCI Characteristic PT NICHD Characteristic SY caDSR Characteristics SY NCI Feature SY NCI Features SY caDSR A term that helps define and render a concept unique. Modifier Qualifier MS NCIT:C41009 Qualifier A term that helps define and render a concept unique. NCI Modifier SY NCI Qualifier PT NCI An active process; excludes processes and mechanisms which fulfill biological functions. Activity General activity MS NCIT:C43431 Activity An active process; excludes processes and mechanisms which fulfill biological functions. NCI Activity PT BRIDG 3.0.3 Activity PT BRIDG 5.3 Activity PT NCI Activity SY caDSR General activity SY caDSR The amount of something per unit size. MS NCIT:C45781 Density The amount of something per unit size. NCI Span a region or interval of distance, space or time. MS NCIT:C68811 Cover Span a region or interval of distance, space or time. NCI An observation in a data set that is numerically distant from the rest of the data. MS NCIT:C79083 Outlier An observation in a data set that is numerically distant from the rest of the data. NCI PSI Extended FASTA Format controlled vocabulary term. MS PEFF:0000001 PEFF CV term PSI Extended FASTA Format controlled vocabulary term. PSI:PEFF CV term that may appear in a PEFF file header section. MS PEFF:0000002 PEFF file header section term CV term that may appear in a PEFF file header section. PSI:PEFF CV term that may appear in a description line of a PEFF file individual sequence entry. MS PEFF:0000003 PEFF file sequence entry term CV term that may appear in a description line of a PEFF file individual sequence entry. PSI:PEFF PEFF keyword for the sequence database name. MS PEFF:0000008 DbName PEFF keyword for the sequence database name. PSI:PEFF PEFF keyword for the sequence database prefix. MS PEFF:0000009 Prefix PEFF keyword for the sequence database prefix. PSI:PEFF PEFF keyword for the sequence database short description. MS PEFF:0000010 DbDescription PEFF keyword for the sequence database short description. PSI:PEFF PEFF keyword for the specifying whether the sequence database is a decoy database. MS PEFF:0000011 Decoy PEFF keyword for the specifying whether the sequence database is a decoy database. PSI:PEFF PEFF keyword for the source of the database file. MS PEFF:0000012 DbSource PEFF keyword for the source of the database file. PSI:PEFF PEFF keyword for the database version (release date) according to database provider. MS PEFF:0000013 DbVersion PEFF keyword for the database version (release date) according to database provider. PSI:PEFF OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider. MS PEFF:0000014 This term was obsoleted. DbDate true OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider. PSI:PEFF PEFF keyword for the sumber of sequence entries in the database. MS PEFF:0000015 NumberOfEntries PEFF keyword for the sumber of sequence entries in the database. PSI:PEFF PEFF keyword for the description of the conversion from original format to this current one. MS PEFF:0000016 Conversion PEFF keyword for the description of the conversion from original format to this current one. PSI:PEFF PEFF keyword for the molecular type of the sequences. MS PEFF:0000017 SequenceType PEFF keyword for the molecular type of the sequences. PSI:PEFF PEFF keyword for database specific keywords not included in the current controlled vocabulary. MS PEFF:0000018 SpecificKey PEFF keyword for database specific keywords not included in the current controlled vocabulary. PSI:PEFF PEFF keyword for the specific values for a custom key. MS PEFF:0000019 SpecificValue PEFF keyword for the specific values for a custom key. PSI:PEFF PEFF keyword for the short description of the PEFF file. MS PEFF:0000020 DatabaseDescription PEFF keyword for the short description of the PEFF file. PSI:PEFF PEFF keyword for a general comment. MS PEFF:0000021 GeneralComment PEFF keyword for a general comment. PSI:PEFF PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms. MS PEFF:0000022 ProteoformDb PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms. PSI:PEFF PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location. MS PEFF:0000023 OptionalTagDef PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location. PSI:PEFF PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation. MS PEFF:0000024 HasAnnotationIdentifiers PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation. PSI:PEFF OBSOLETE Sequence database unique identifier. MS PEFF:0001001 This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. DbUniqueId true OBSOLETE Sequence database unique identifier. PSI:PEFF PEFF keyword for the protein full name. MS PEFF:0001002 PName PEFF keyword for the protein full name. PSI:PEFF PEFF keyword for the NCBI taxonomy identifier. MS PEFF:0001003 NcbiTaxId PEFF keyword for the NCBI taxonomy identifier. PSI:PEFF PEFF keyword for the taxonomy name (latin or common name). MS PEFF:0001004 TaxName PEFF keyword for the taxonomy name (latin or common name). PSI:PEFF PEFF keyword for the gene name. MS PEFF:0001005 GName PEFF keyword for the gene name. PSI:PEFF PEFF keyword for the sequence length. MS PEFF:0001006 Length PEFF keyword for the sequence length. PSI:PEFF PEFF keyword for the sequence version. MS PEFF:0001007 SV PEFF keyword for the sequence version. PSI:PEFF PEFF keyword for the entry version. MS PEFF:0001008 EV PEFF keyword for the entry version. PSI:PEFF PEFF keyword for the Protein Evidence; A UniProtKB code 1-5. MS PEFF:0001009 PE PEFF keyword for the Protein Evidence; A UniProtKB code 1-5. PSI:PEFF PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains. MS PEFF:0001010 Processed PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains. PSI:PEFF OBSOLETE Sequence variation (substitution, insertion, deletion). MS PEFF:0001011 This term was made obsolete in favor of VariantSimple and VariantComplex. Variant true OBSOLETE Sequence variation (substitution, insertion, deletion). PSI:PEFF PEFF keyword for the modified residue with PSI-MOD identifier. MS PEFF:0001012 ModResPsi PEFF keyword for the modified residue with PSI-MOD identifier. PSI:PEFF PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier. MS PEFF:0001013 ModRes PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier. PSI:PEFF PEFF keyword for the Alternative Accession Code. MS PEFF:0001014 AltAC PEFF keyword for the Alternative Accession Code. PSI:PEFF PEFF keyword for the sequence status. Complete or Fragment. MS PEFF:0001015 SeqStatus PEFF keyword for the sequence status. Complete or Fragment. PSI:PEFF PEFF keyword for the entry associated comment. MS PEFF:0001016 CC PEFF keyword for the entry associated comment. PSI:PEFF PEFF keyword for the entry associated keyword(s). MS PEFF:0001017 KW PEFF keyword for the entry associated keyword(s). PSI:PEFF PEFF keyword for the Gene Ontology code. MS PEFF:0001018 GO PEFF keyword for the Gene Ontology code. PSI:PEFF PEFF keyword for the cross-reference to an external resource. MS PEFF:0001019 XRef PEFF keyword for the cross-reference to an external resource. PSI:PEFF Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed. MS PEFF:0001020 mature protein Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed. PSI:PEFF Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein. MS PEFF:0001021 signal peptide Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein. PSI:PEFF Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle. MS PEFF:0001022 transit peptide Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle. PSI:PEFF PEFF keyword for the sequence conflict; a UniProtKB term. MS PEFF:0001023 Conflict PEFF keyword for the sequence conflict; a UniProtKB term. PSI:PEFF PEFF keyword for the Sequence checksum in crc64. MS PEFF:0001024 Crc64 PEFF keyword for the Sequence checksum in crc64. PSI:PEFF PEFF keyword for the sequence range of a domain. MS PEFF:0001025 Domain PEFF keyword for the sequence range of a domain. PSI:PEFF PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term. MS PEFF:0001026 ID PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term. PSI:PEFF PEFF keyword for the modified residue with UniMod identifier. MS PEFF:0001027 ModResUnimod PEFF keyword for the modified residue with UniMod identifier. PSI:PEFF PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term. MS PEFF:0001028 VariantSimple PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term. PSI:PEFF PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon. MS PEFF:0001029 VariantComplex PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon. PSI:PEFF PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers. MS PEFF:0001030 Proteoform PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers. PSI:PEFF PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications. MS PEFF:0001031 DisulfideBond PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications. PSI:PEFF PEFF keyword describing the type of processing event being described. MS PEFF:0001032 PEFF molecule processing keyword PEFF keyword describing the type of processing event being described. PSI:PEFF PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary. MS PEFF:0001033 Comment PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary. PSI:PEFF Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide. MS PEFF:0001034 propeptide Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide. PSI:PEFF N-terminal methionine residue of a protein that can be co-translationally cleaved. MS PEFF:0001035 initiator methionine N-terminal methionine residue of a protein that can be co-translationally cleaved. PSI:PEFF ([0-9]+|[A-Z*](|.+)?). MS PEFF:1002001 regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment ([0-9]+|[A-Z*](|.+)?). PSI:PEFF (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+). MS PEFF:1002002 regular expression for PEFF molecular sequence type (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+). PSI:PEFF (Complete|Fragment|[a-z0-9A-Z]+). MS PEFF:1002003 regular expression for PEFF sequence status (Complete|Fragment|[a-z0-9A-Z]+). PSI:PEFF A unit of measurement is a standardized quantity of a physical quality. george gkoutos unit.ontology UO:0000000 unit A unit of measurement is a standardized quantity of a physical quality. Wikipedia:Wikipedia A unit which is a standard measure of the distance between two points. george gkoutos unit.ontology UO:0000001 length unit A unit which is a standard measure of the distance between two points. Wikipedia:Wikipedia A unit which is a standard measure of the amount of matter/energy of a physical object. george gkoutos unit.ontology UO:0000002 mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. Wikipedia:Wikipedia A unit which is a standard measure of the dimension in which events occur in sequence. george gkoutos UO:0000149 time derived unit unit.ontology UO:0000003 time unit A unit which is a standard measure of the dimension in which events occur in sequence. Wikipedia:Wikipedia A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. george gkoutos UO:0000126 temperature derived unit unit.ontology UO:0000005 temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. Wikipedia:Wikipedia A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. george gkoutos m metre unit.ontology UO:0000008 meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. BIPM:BIPM NIST:NIST A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. george gkoutos s unit.ontology UO:0000010 second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. BIPM:BIPM NIST:NIST A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. george gkoutos K unit.ontology UO:0000012 kelvin A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. BIPM:BIPM NIST:NIST A length unit which is equal to one millionth of a meter or 10^[-6] m. george gkoutos micrometre micron um unit.ontology UO:0000017 micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. NIST:NIST A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. george gkoutos nanometre nm unit.ontology UO:0000018 nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. NIST:NIST A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. george gkoutos g unit.ontology UO:0000021 gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. NIST:NIST A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. george gkoutos C unit.ontology UO:0000027 degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. NIST:NIST A time unit which is equal to one thousandth of a second or 10^[-3] s. george gkoutos ms unit.ontology UO:0000028 millisecond A time unit which is equal to one thousandth of a second or 10^[-3] s. NIST:NIST A time unit which is equal to 60 seconds. george gkoutos min unit.ontology UO:0000031 minute A time unit which is equal to 60 seconds. Wikipedia:Wikipedia A unit which is one of a particular measure to which all measures of that type can be related. george gkoutos unit.ontology UO:0000045 base unit A unit which is one of a particular measure to which all measures of that type can be related. NIST:NIST A unit which is a standard measure of the amount of a 2-dimensional flat surface. george gkoutos unit.ontology UO:0000047 area unit A unit which is a standard measure of the amount of a 2-dimensional flat surface. UOC:GVG A density unit which is a standard measure of the mass of a substance in a given volume. george gkoutos mass per unit volume unit.ontology UO:0000052 mass density unit A density unit which is a standard measure of the mass of a substance in a given volume. UOC:GVG A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. george gkoutos unit.ontology UO:0000095 volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. NIST:NIST A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. george gkoutos millilitre ml unit.ontology UO:0000098 milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. NIST:NIST A unit which is a standard measure of the number of repetitive actions in a particular time. george gkoutos unit.ontology UO:0000105 frequency unit A unit which is a standard measure of the number of repetitive actions in a particular time. NIST:NIST A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. george gkoutos Hz s^1 unit.ontology UO:0000106 hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. NIST:NIST A unit which is a standard measure of the force applied to a given area. george gkoutos unit.ontology UO:0000109 pressure unit A unit which is a standard measure of the force applied to a given area. NIST:NIST A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]. george gkoutos Pa unit.ontology UO:0000110 pascal A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]. NIST:NIST A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc). george gkoutos unit.ontology UO:0000111 energy unit A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc). NIST:NIST An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force. george gkoutos J unit.ontology UO:0000112 joule An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force. NIST:NIST A unit which is a standard measure of the figure or space formed by the junction of two lines or planes. george gkoutos unit.ontology UO:0000121 angle unit A unit which is a standard measure of the figure or space formed by the junction of two lines or planes. Wikipedia:Wikipedia A unit which is a standard measure of the angle formed by two straight lines in the same plane. george gkoutos unit.ontology UO:0000122 plane angle unit A unit which is a standard measure of the angle formed by two straight lines in the same plane. Wikipedia:Wikipedia true true A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s. george gkoutos ns unit.ontology UO:0000150 nanosecond A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s. NIST:NIST A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance. george gkoutos unit.ontology UO:0000166 parts per notation unit A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance. Wikipedia:Wikipedia A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]. george gkoutos 10^[-6] ppm unit.ontology UO:0000169 parts per million A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]. UOC:GVG A mass unit density which is equal to mass of an object in grams divided by the volume in liters. george gkoutos g/L gram per litre unit.ontology UO:0000175 gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. UOC:GVG A unit which is a standard measure of the influence exerted by some mass. george gkoutos unit.ontology UO:0000182 density unit A unit which is a standard measure of the influence exerted by some mass. Wikipedia:Wikipedia A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad. george gkoutos unit.ontology UO:0000185 degree A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad. Wikipedia:Wikipedia A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. george gkoutos unit.ontology UO:0000186 dimensionless unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. Wikipedia:Wikipedia A dimensionless ratio unit which denotes numbers as fractions of 100. george gkoutos % unit.ontology UO:0000187 percent A dimensionless ratio unit which denotes numbers as fractions of 100. Wikipedia:Wikipedia A dimensionless unit which denotes a simple count of things. george gkoutos count unit.ontology UO:0000189 count unit A dimensionless unit which denotes a simple count of things. MGED:MGED A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. george gkoutos unit.ontology UO:0000190 ratio A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. Wikipedia:Wikipedia A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). george gkoutos unit.ontology UO:0000191 fraction A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). Wikipedia:Wikipedia A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field. george gkoutos unit.ontology UO:0000217 electric potential difference unit A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field. Wikipedia:Wikipedia An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy. george gkoutos V unit.ontology UO:0000218 volt An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy. Wikipedia:Wikipedia An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state. george gkoutos Da amu u unified atomic mass unit unit.ontology UO:0000221 dalton An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state. Wikipedia:Wikipedia A mass unit which is equal to one thousand daltons. george gkoutos kDa unit.ontology UO:0000222 kilodalton A mass unit which is equal to one thousand daltons. Wikipedia:Wikipedia A unit which is a standard measure of the strength of a magnetic field. george gkoutos B unit.ontology UO:0000227 magnetic flux density unit A unit which is a standard measure of the strength of a magnetic field. allnet:allnet A magnetic flux density unit which is equal to one weber per square meter. george gkoutos T Wb/m2 unit.ontology UO:0000228 tesla A magnetic flux density unit which is equal to one weber per square meter. WordNet:WordNet A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J. george gkoutos eV electron volt unit.ontology UO:0000266 electronvolt A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J. Wikipedia:Wikipedia The electric field strength is a unit which is a measure of the potential difference between two points some distance apart. george gkoutos 2009-03-03T12:23:16Z E-field strength unit.ontology UO:0000267 electric field strength unit The electric field strength is a unit which is a measure of the potential difference between two points some distance apart. Wikipedia:http://en.wikipedia.org/wiki/Electric_field The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart. george gkoutos 2009-03-03T12:28:17Z V/m volt per metre unit.ontology UO:0000268 volt per meter The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart. Wikipedia:http://en.wikipedia.org/wiki/Electric_field A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light. george gkoutos 2009-07-14T12:33:48Z AU unit.ontology UO:0000269 absorbance unit A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light. Wikipedia:http://en.wikipedia.org/wiki/Absorbance A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . george gkoutos unit.ontology UO:0000270 volumetric flow rate unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . Wikipedia:Wikipedia A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. george gkoutos microlitres per minute uL/min unit.ontology UO:0000271 microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. UOC:GVG An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long. gkoutos 2013-06-27T05:06:40Z unit.ontology A^[2] UO:0000324 square angstrom An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long. UOC:GVG A practiced and regimented skill or series of actions. MS NCIT:C16847 Technique A practiced and regimented skill or series of actions. NCI A method of analyzing or representing statistical data; a procedure for calculating a statistic. MS NCIT:C19044 Statistical Technique A method of analyzing or representing statistical data; a procedure for calculating a statistic. NCI One of the axes representing the projection of varience resulting from principal component analysis. MS NCIT:C60694 Principal Component One of the axes representing the projection of varience resulting from principal component analysis. NCI