format-version: 1.2
date: 07:07:2008 14:30
saved-by: David Sparkman
auto-generated-by: OBO-Edit 1.101
default-namespace: MS
remark: namespace: MS
remark: version: 1.9.0
remark: release date: 2008-11-25
remark: coverage: Mass spectrometer output files
remark: creator: Matt Chambers <matt.chambers <@> vanderbilt.edu>
remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group
remark: 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.
import: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo?revision=1.15

[Term]
id: MS:0000000
name: Proteomics Standards Initiative Mass Spectrometry Ontology
def: "Proteomics Standards Initiative Mass Spectrometry Ontology." [PSI:MS]

[Term]
id: MS:1000001
name: sample number
def: "A reference number relevant to the sample under study." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute

[Term]
id: MS:1000002
name: sample name
def: "A reference string relevant to the sample under study." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000003
name: sample state
def: "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000004
name: sample mass
def: "Total mass of sample used." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000005
name: sample volume
def: "Total volume of solution used." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000095 ! volume unit

[Term]
id: MS:1000006
name: sample concentration
def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute
relationship: has_units UO:0000051 ! concentration unit

[Term]
id: MS:1000007
name: inlet type
def: "The nature of the sample inlet." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1000008
name: ionization type
def: "The method by which gas phase ions are generated from the sample." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1000009
name: ionization mode
def: "Whether positive or negative ions are selected for analysis by the spectrometer. Re-map to Polarity Mode." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000010
name: analyzer type
def: "The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000011
name: mass resolution
def: "The maximum m/z value at which two peaks can be resolved, according to one of the standard measures." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000012
name: resolution measurement method
def: "Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS]
is_a: MS:1000596 ! measurement method

[Term]
id: MS:1000013
name: resolution type
def: "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]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000014
name: accuracy
def: "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000166 ! parts per notation

[Term]
id: MS:1000015
name: scan rate
def: "Rate in (m/z)/sec for scanning analyzers." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1000016
name: scan time
def: "The time that an analyzer started a scan, relative to the start of the run." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000003 ! time unit

[Term]
id: MS:1000017
name: Scan Function
def: "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]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000018
name: scan direction
def: "Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS]
relationship: part_of MS:1000441 ! scan

[Term]
id: MS:1000019
name: scan law
def: "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]
relationship: part_of MS:1000441 ! scan

[Term]
id: MS:1000020
name: scanning method
def: "Describes the acquisition data type produced by a tandem mass spectrometry experiment." [PSI:MS]
synonym: "Tandem Scanning Method" RELATED []
relationship: part_of MS:1000441 ! scan

[Term]
id: MS:1000021
name: reflectron state
def: "Status of the reflectron, turned on or off." [PSI:MS]
is_a: MS:1000480 ! mass analyzer attribute

[Term]
id: MS:1000022
name: TOF Total Path Length
def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000001 ! length unit

[Term]
id: MS:1000023
name: isolation width
def: "The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000024
name: final MS exponent
def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute

[Term]
id: MS:1000025
name: magnetic field strength
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "B" EXACT []
synonym: "Magnetic Field" RELATED []
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000227 ! magnetic flux density

[Term]
id: MS:1000026
name: detector type
def: "Type of detector used in the mass spectrometer." [PSI:MS]
relationship: part_of MS:1000453 ! detector

[Term]
id: MS:1000027
name: detector acquisition mode
def: "Method by which detector signal is acquired by the data system." [PSI:MS]
relationship: part_of MS:1000453 ! detector

[Term]
id: MS:1000028
name: detector resolution
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000481 ! detector attribute

[Term]
id: MS:1000029
name: sampling frequency
def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "ADC Sampling Frequency" NARROW []
is_a: MS:1000481 ! detector attribute

[Term]
id: MS:1000030
name: vendor
def: "Name of instrument vendor, replaced by MS:1000031 Model From Vendor." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000031
name: instrument model
def: "Instrument model name not including the vendor's name." [PSI:MS]
relationship: part_of MS:1000463 ! instrument

[Term]
id: MS:1000032
name: customization
def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000496 ! instrument attribute

[Term]
id: MS:1000033
name: deisotoping
def: "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000034
name: charge deconvolution
def: "The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions." [PSI:MS]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000035
name: peak picking
def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data." [PSI:MS]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000036
name: scan mode
def: "TODO: Add definition." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000037
name: polarity
def: "Terms to describe the polarity setting of the instrument." [PSI:MS]
relationship: part_of MS:1000459 ! spectrum instrument description

[Term]
id: MS:1000038
name: minute
def: "Acquisition time in minutes. Replace by MS:1000016 - Scan Time." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000039
name: second
def: "Acquisition time in seconds. Replace by MS:1000016 - Scan Time." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000040
name: m/z
def: "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]
synonym: "mass-to-charge ratio" EXACT []
synonym: "Th" EXACT []
synonym: "thomson" EXACT []
is_a: MS:1000460 ! unit

[Term]
id: MS:1000041
name: charge state
def: "The charge state of the ion, single or multiple and positive or negatively charged." [PSI:MS]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute

[Term]
id: MS:1000042
name: intensity
def: "Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute

[Term]
id: MS:1000043
name: intensity unit
def: "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]
is_a: MS:1000460 ! unit

[Term]
id: MS:1000044
name: dissociation method
def: "Fragmentation method used for dissociation or fragmentation." [PSI:MS]
synonym: "Activation Method" RELATED []
relationship: part_of MS:1000456 ! precursor activation

[Term]
id: MS:1000045
name: collision energy
def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000111 ! energy unit

[Term]
id: MS:1000046
name: energy unit
def: "Energy units are represented in either eV or Joules. Obsoleted in favor of UO:0000111" [PSI:MS]
is_a: MS:1000460 ! unit
is_obsolete: true

[Term]
id: MS:1000047
name: emulsion
def: "State if the sample is in emulsion form." [PSI:MS]
is_a: MS:1000003 ! sample state

[Term]
id: MS:1000048
name: gas
def: "State if the sample is in gaseous form." [PSI:MS]
is_a: MS:1000003 ! sample state

[Term]
id: MS:1000049
name: liquid
def: "State if the sample is in liquid form." [PSI:MS]
is_a: MS:1000003 ! sample state

[Term]
id: MS:1000050
name: solid
def: "State if the sample is in solid form." [PSI:MS]
is_a: MS:1000003 ! sample state

[Term]
id: MS:1000051
name: solution
def: "State if the sample is in solution form." [PSI:MS]
is_a: MS:1000003 ! sample state

[Term]
id: MS:1000052
name: suspension
def: "State if the sample is in suspension form." [PSI:MS]
is_a: MS:1000003 ! sample state

[Term]
id: MS:1000053
name: sample batch
def: "Sample batch lot identifier." [PSI:MS]
is_a: MS:1000548 ! sample attribute
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000054
name: chromatography
def: "Chromatographic conditions used to obtain the sample." [PSI:MS]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000055
name: continuous flow fast atom bombardment
def: "Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix." [PSI:MS]
synonym: "CF-FAB" EXACT []
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000056
name: direct inlet
def: "The sample is directly inserted into the ion source, usually on the end of a heatable probe." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000057
name: electrospray inlet
def: "Inlet used for introducing the liquid sample into an electrospray ionization source." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000058
name: flow injection analysis
def: "Sample is directly injected or infused into the ionization source." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000059
name: inductively coupled plasma
def: "A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000060
name: infusion
def: "The continuous flow of solution of a sample into the ionization source." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000061
name: jet separator
def: "A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000062
name: membrane separator
def: "A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000063
name: moving belt
def: "Continuous moving surface in the form of a belt which passes through an ionsource carrying analyte molecules." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000064
name: moving wire
def: "Continuous moving surface in the form of a wire which passes through an ionsource carrying analyte molecules." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000065
name: open split
def: "A division of flowing stream of liquid into two streams." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000066
name: particle beam
def: "Method for generating ions from a solution of an analyte." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000067
name: reservoir
def: "A sample inlet method involving a reservoir." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000068
name: septum
def: "A disc composed of a flexible material that seals the entrance to the reservoir. Can also be enterance to the vaccum chamber." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000069
name: thermospray inlet
def: "A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000070
name: atmospheric pressure chemical ionization
def: "Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization." [PSI:MS]
synonym: "APCI" EXACT []
is_a: MS:1000240 ! atmospheric pressure ionization

[Term]
id: MS:1000071
name: chemical ionization
def: "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]
synonym: "CI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000072
name: Electronic Ionization
def: "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. OBSOLETE because redundant replaced by MS:1000389 electron ionization" [PSI:MS]
synonym: "EI" EXACT []
is_obsolete: true

[Term]
id: MS:1000073
name: electrospray ionization
def: "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]
synonym: "ESI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000074
name: fast atom bombardment ionization
def: "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]
synonym: "FAB" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000075
name: matrix-assisted laser desorption ionization
def: "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]
synonym: "MALDI" EXACT []
is_a: MS:1000247 ! desorption ionization

[Term]
id: MS:1000076
name: negative ion mode
def: "TODO: Add defintion." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000077
name: positive ion mode
def: "TODO: Add definition." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000078
name: axial ejection linear ion trap
def: "A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS]
is_a: MS:1000264 ! ion trap

[Term]
id: MS:1000079
name: fourier transform ion cyclotron resonance mass spectrometer
def: "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]
synonym: "FT_ICR" EXACT []
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000080
name: magnetic sector
def: "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]
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000081
name: quadrupole
def: "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]
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000082
name: quadrupole ion trap
def: "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]
synonym: "Paul Ion trap" EXACT []
synonym: "QIT" EXACT []
synonym: "Quistor" EXACT []
is_a: MS:1000264 ! ion trap

[Term]
id: MS:1000083
name: radial ejection linear ion trap
def: "A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS]
is_a: MS:1000264 ! ion trap

[Term]
id: MS:1000084
name: time-of-flight
def: "Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS]
synonym: "TOF" EXACT []
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000085
name: baseline
def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS]
is_a: MS:1000012 ! resolution measurement method

[Term]
id: MS:1000086
name: full width at half-maximum
def: "A measure of resolution represented as width of the peak at half peak height." [PSI:MS]
synonym: "FWHM" EXACT []
is_a: MS:1000012 ! resolution measurement method

[Term]
id: MS:1000087
name: ten percent valley
def: "An attribute of resolution when the ratio between adjacent signals is 10% of the signal height." [PSI:MS]
is_a: MS:1000012 ! resolution measurement method

[Term]
id: MS:1000088
name: constant
def: "When resolution is constant with respect to m/z." [PSI:MS]
is_a: MS:1000013 ! resolution type

[Term]
id: MS:1000089
name: proportional
def: "When resolution is proportional with respect to m/z." [PSI:MS]
is_a: MS:1000013 ! resolution type

[Term]
id: MS:1000090
name: mass scan
def: "A variation of instrument where a selected mass is scanned." [PSI:MS]
is_a: MS:1000017 ! Scan Function

[Term]
id: MS:1000091
name: selected ion detection
def: "Please see Single Ion Monitoring." [PSI:MS]
is_a: MS:1000017 ! Scan Function

[Term]
id: MS:1000092
name: decreasing m/z scan
def: "High to low direction in terms of m/z of the scan for scanning analyzers." [PSI:MS]
is_a: MS:1000018 ! scan direction

[Term]
id: MS:1000093
name: increasing m/z scan
def: "Low to high direction in terms of m/z of the scan for scanning analyzers." [PSI:MS]
is_a: MS:1000018 ! scan direction

[Term]
id: MS:1000094
name: exponential
def: "The mass scan is done in exponential mode." [PSI:MS]
is_a: MS:1000019 ! scan law

[Term]
id: MS:1000095
name: linear
def: "The mass scan is done in linear mode." [PSI:MS]
is_a: MS:1000019 ! scan law

[Term]
id: MS:1000096
name: quadratic
def: "The mass scan is done in quadratic mode." [PSI:MS]
is_a: MS:1000019 ! scan law

[Term]
id: MS:1000097
name: constant neutral mass loss
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000098
name: multiple ion monitoring
def: "Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring." [PSI:MS]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000099
name: multiple reaction monitoring
def: "This term is not recommended. See Selected Reaction Monitoring. Replace by MS:1000206 - Selected Reaction Monitoring." [PSI:MS]
synonym: "MRM" EXACT []
is_obsolete: true

[Term]
id: MS:1000100
name: precursor ion scan
def: "The specific scan function or process that will record a precursor ion spectrum." [PSI:MS]
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000101
name: product ion scan
def: "The specific scan function or process that records product ion spectrum." [PSI:MS]
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000102
name: single ion monitoring
def: "The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum. Remap to MS:1000205." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000103
name: single reaction monitoring
def: "See Selected Reaction Monitoring. remap to MS:1000102." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000104
name: None  ??
def: "None." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000105
name: reflectron off
def: "Reflectron is off." [PSI:MS]
is_a: MS:1000021 ! reflectron state

[Term]
id: MS:1000106
name: reflectron on
def: "Reflectron is on." [PSI:MS]
is_a: MS:1000021 ! reflectron state

[Term]
id: MS:1000107
name: channeltron
def: "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]
synonym: "Channeltron Detector" EXACT []
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000108
name: conversion dynode electron multiplier
def: "A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected." [PSI:MS]
is_a: MS:1000346 ! conversion dynode

[Term]
id: MS:1000109
name: conversion dynode photomultiplier
def: "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]
synonym: "ion-to-photon detector" RELATED []
is_a: MS:1000346 ! conversion dynode

[Term]
id: MS:1000110
name: daly detector
def: "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]
synonym: "Daly" EXACT []
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000111
name: electron multiplier tube
def: "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]
synonym: "EMT" EXACT []
is_a: MS:1000253 ! electron multiplier

[Term]
id: MS:1000112
name: faraday cup
def: "A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device." [PSI:MS]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000113
name: focal plane array
def: "An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS]
is_a: MS:1000348 ! focal plane collector

[Term]
id: MS:1000114
name: microchannel plate detector
def: "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]
synonym: "multichannel plate" EXACT []
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000115
name: multi-collector
def: "A detector system commonly used in inductively coupled plasma mass spectrometers." [PSI:MS]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000116
name: photomultiplier
def: "A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected." [PSI:MS]
synonym: "PMT" EXACT []
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000117
name: analog-digital converter
def: "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]
synonym: "ADC" EXACT []
is_a: MS:1000027 ! detector acquisition mode

[Term]
id: MS:1000118
name: pulse counting
def: "Definition to do." [PSI:MS]
is_a: MS:1000027 ! detector acquisition mode

[Term]
id: MS:1000119
name: time-digital converter
def: "A device for converting a signal of sporadic pluses into a digital representation of their time indices." [PSI:MS]
synonym: "TDC" EXACT []
is_a: MS:1000027 ! detector acquisition mode

[Term]
id: MS:1000120
name: transient recorder
def: "A detector acquisition mode used for detecting transient signals." [PSI:MS]
is_a: MS:1000027 ! detector acquisition mode

[Term]
id: MS:1000121
name: AB SCIEX instrument model
def: "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]
synonym: "Applied Biosystems|MDS SCIEX" RELATED []
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000122
name: Bruker Daltonics instrument model
def: "Bruker Daltonics instrument model." [PSI:MS]
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000123
name: IonSpec instrument model
def: "IonSpec corporation instrument model." [PSI:MS]
is_a: MS:1000489 ! Varian instrument model

[Term]
id: MS:1000124
name: Shimadzu instrument model
def: "Shimadzu corporation instrument model." [PSI:MS]
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000125
name: Thermo Finnigan instrument model
def: "ThermoFinnigan from Thermo Electron Corporation instrument model." [PSI:MS]
is_a: MS:1000483 ! Thermo Fisher Scientific instrument model

[Term]
id: MS:1000126
name: Waters instrument model
def: "Waters Corporation instrument model." [PSI:MS]
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000127
name: centroid mass spectrum
def: "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS]
synonym: "Discrete Mass Spectrum" EXACT []
is_a: MS:1000525 ! spectrum representation

[Term]
id: MS:1000128
name: profile mass spectrum
def: "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]
synonym: "continuous mass spectrum" EXACT []
synonym: "Continuum Mass Spectrum" EXACT []
is_a: MS:1000525 ! spectrum representation

[Term]
id: MS:1000129
name: negative scan
def: "Polarity of the scan is negative." [PSI:MS]
is_a: MS:1000037 ! polarity
is_a: MS:1000465 ! scan polarity

[Term]
id: MS:1000130
name: positive scan
def: "Polarity of the scan is positive." [PSI:MS]
is_a: MS:1000037 ! polarity
is_a: MS:1000465 ! scan polarity

[Term]
id: MS:1000131
name: number of counts
def: "The number of counted events observed in one or a group of elements of a detector." [PSI:MS]
is_a: MS:1000043 ! intensity unit

[Term]
id: MS:1000132
name: percent of base peak
def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000043 ! intensity unit

[Term]
id: MS:1000133
name: collision-induced dissociation
def: "The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended." [PSI:MS]
synonym: "CID" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000134
name: plasma desorption
def: "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]
synonym: "PD" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000135
name: post-source decay
def: "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]
synonym: "PSD" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000136
name: surface-induced dissociation
def: "Fragmentation that results from the collision of an ion with a surface." [PSI:MS]
synonym: "SID" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000137
name: electron volt
def: "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]
synonym: "eV" EXACT []
is_obsolete: true

[Term]
id: MS:1000138
name: percent collision energy
def: "Collision energy required to fragment an ion represented as a percent value." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: UO:0000111 ! energy unit

[Term]
id: MS:1000139
name: 4000 Q TRAP
def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000140
name: 4700 Proteomics Analyzer
def: "Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS]
is_a: MS:1000495 ! Applied Biosystems instrument model

[Term]
id: MS:1000141
name: APEX IV
def: "Bruker Daltonics APEX IV MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000142
name: APEX-Q
def: "Bruker Daltonics APEX-Q MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000143
name: API 150EX
def: "Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000144
name: API 150EX Prep
def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000145
name: API 2000
def: "Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000146
name: API 3000
def: "Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000147
name: API 4000
def: "Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000148
name: autoFlex II
def: "Bruker Daltonics autoFlex II MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000149
name: autoFlex TOF/TOF
def: "Bruker Daltonics autoFlex TOF/TOF MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000150
name: Auto Spec Ultima NT
def: "Waters AutoSpec Ultima NT MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000151
name: Bio TOF II
def: "Bruker Daltonics BioTOF II MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000152
name: Bio TOF Q
def: "Bruker Daltonics BioTOF Q MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000153
name: DELTA plusAdvantage
def: "ThermoFinnigan DELTA plusAdvantage MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000154
name: DELTAplusXP
def: "ThermoFinnigan DELTAplusXP MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000155
name: ELEMENT2
def: "ThermoFinnigan ELEMENT2 MS." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000156
name: esquire4000
def: "Bruker Daltonics esquire4000 MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000157
name: esquire6000
def: "Bruker Daltonics esquire6000 MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000158
name: explorer
def: "IonSpec Explorer MS." [PSI:MS]
is_a: MS:1000123 ! IonSpec instrument model

[Term]
id: MS:1000159
name: GCT
def: "Waters GCT MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000160
name: HCT
def: "Bruker Daltonics HCT MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000161
name: HCT Plus
def: "Bruker Daltonics HCTPlus MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000162
name: HiRes ESI
def: "IonSpec HiResESI MS." [PSI:MS]
is_a: MS:1000123 ! IonSpec instrument model

[Term]
id: MS:1000163
name: HiRes MALDI
def: "IonSpec HiResMALDI MS." [PSI:MS]
is_a: MS:1000123 ! IonSpec instrument model

[Term]
id: MS:1000164
name: IsoPrime
def: "Waters IsoPrime MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000165
name: IsoProbe
def: "Waters IsoProbe MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000166
name: IsoProbe T
def: "Waters IsoProbe T MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000167
name: LCQ Advantage
def: "ThermoFinnigan LCQ Advantage MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000168
name: LCQ Classic
def: "ThermoFinnigan LCQ Classic MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000169
name: LCQ Deca XP Plus
def: "ThermoFinnigan LCQ Deca XP Plus MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000170
name: M@LDI L
def: "Waters MALDI L MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000171
name: M@LDI LR
def: "Waters MALDI LR MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000172
name: MAT253
def: "ThermoFinnigan MAT253 MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000173
name: MAT900XP
def: "ThermoFinnigan MAT900XP MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000174
name: MAT900XP Trap
def: "ThermoFinnigan MAT900XP Trap MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000175
name: MAT95XP
def: "ThermoFinnigan MAT95XP MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000176
name: MAT95XP Trap
def: "ThermoFinnigan MAT95XP Trap MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000177
name: microFlex
def: "Bruker Daltonics microFlex MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000178
name: microTOFLC
def: "Bruker Daltonics microTOFLC MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000179
name: neptune
def: "ThermoFinnigan NEPTUNE MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000180
name: NG-5400
def: "Waters NG-5400 MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000181
name: OMEGA
def: "IonSpec OMEGA MS." [PSI:MS]
is_a: MS:1000123 ! IonSpec instrument model

[Term]
id: MS:1000182
name: OMEGA-2001
def: "IonSpec OMEGA-2001 MS." [PSI:MS]
is_a: MS:1000123 ! IonSpec instrument model

[Term]
id: MS:1000183
name: OmniFlex
def: "Bruker Daltonics OminFlex MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000184
name: Platform ICP
def: "Waters Platform ICP MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000185
name: PolarisQ
def: "ThermoFinnigan PolarisQ MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000186
name: proteomics solution 1
def: "Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000187
name: Q TRAP
def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000188
name: Q-Tof micro
def: "Waters Q-Tof micro MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000189
name: Q-Tof ultima
def: "Waters Q-Tof Ultima MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000190
name: QSTAR
def: "Applied Biosystems/MDS SCIEX QSTAR MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000191
name: quattro micro
def: "Waters Quattro micro MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000192
name: Quattro UItima
def: "Waters Quattro Uitima MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000193
name: Surveyor MSQ
def: "ThermoFinnigan Surveyor MSQ MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000194
name: SymBiot I
def: "Applied Biosystems/MDS SCIEX SymBiot I MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000195
name: SymBiot XVI
def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000196
name: TEMPUS TOF
def: "ThermoFinnigan TEMPUS TOF MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000197
name: TRACE DSQ
def: "ThermoFinnigan TRACE DSQ MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000198
name: TRITON
def: "ThermoFinnigan TRITON MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000199
name: TSQ Quantum
def: "ThermoFinnigan TSQ Quantum MS." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000200
name: ultima
def: "IonSpec Ultima MS." [PSI:MS]
is_a: MS:1000123 ! IonSpec instrument model

[Term]
id: MS:1000201
name: ultraFlex
def: "Bruker Daltonics ultraFlex MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000202
name: ultraFlex TOF/TOF
def: "Bruker Daltonics ultraFlex TOF/TOF MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000203
name: Voyager-DE PRO
def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS." [PSI:MS]
is_a: MS:1000495 ! Applied Biosystems instrument model

[Term]
id: MS:1000204
name: Voyager-DE STR
def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS." [PSI:MS]
is_a: MS:1000495 ! Applied Biosystems instrument model

[Term]
id: MS:1000205
name: selected ion monitoring
def: "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]
synonym: "MIM" RELATED []
synonym: "Multiple Ion Monitoring" EXACT []
synonym: "SIM" EXACT []
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000206
name: selected reaction monitoring
def: "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]
synonym: "MRM" RELATED []
synonym: "Multiple Reaction Monitoring" RELATED []
synonym: "SRM" EXACT []
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000207
name: accurate mass
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000208
name: average mass
def: "The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000209
name: appearance energy
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "AE" EXACT []
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000111 ! energy unit

[Term]
id: MS:1000210
name: base peak
def: "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]
synonym: "BP" EXACT []
is_a: MS:1000231 ! peak

[Term]
id: MS:1000211
name: charge number
def: "The total charge on an ion divided by the electron charge e." [PSI:MS]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
synonym: "z" EXACT []
is_a: MS:1000507 ! ion attribute

[Term]
id: MS:1000212
name: dalton
def: "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]
synonym: "Da" EXACT []
is_obsolete: true

[Term]
id: MS:1000213
name: electron affinity
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "EA" EXACT []
is_a: MS:1000507 ! ion attribute

[Term]
id: MS:1000214
name: electron energy obsolete
def: "The potential difference through which electrons are accelerated before they are used to bring about electron ionization." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000215
name: exact mass
def: "The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000216
name: field-free region
def: "A section of a mass spectrometer in which there are no electric or magnetic fields." [PSI:MS]
synonym: "FFR" EXACT []
is_a: MS:1000487 ! ion optics attribute

[Term]
id: MS:1000217
name: ionization cross section
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000218
name: ioniazation efficiency
def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used. See Ionization Efficiency." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_obsolete: true

[Term]
id: MS:1000219
name: ionization energy
def: "The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "IE" EXACT []
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000111 ! energy unit

[Term]
id: MS:1000220
name: isotope dilution mass spectrometry
def: "A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard." [PSI:MS]
synonym: "IDMS" EXACT []
is_a: MS:1000268 ! mass spectrometry

[Term]
id: MS:1000221
name: magnetic deflection
def: "The deflection of charged particles in a magnetic field due to a force equal to qv B 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]
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000222
name: mass defect
def: "The difference between the monoisotipic and nominal mass of a molecule or atom." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000223
name: mass number
def: "The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute

[Term]
id: MS:1000224
name: molecular mass
def: "The mass of one mole of a molecular substance (6.022 1415(10) x 10^23 molecules)." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000225
name: monoisotopic mass
def: "The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000226
name: molecular beam mass spectrometry
def: "A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam." [PSI:MS]
synonym: "MBMS" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000227
name: multiphoton ionization
def: "Photoionization of an atom or molecule in which in two or more photons are absorbed." [PSI:MS]
synonym: "MPI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000228
name: nitrogen rule
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000229
name: nominal mass
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000002 ! mass unit

[Term]
id: MS:1000230
name: odd-electron rule
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000231
name: peak
def: "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]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000232
name: peak intensity
def: "The height or area of a peak in a mass spectrum. Replaced by MS:1000505 Base Peak Intensity." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000233
name: proton affinity
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "PA" EXACT [PSI:MS]
is_a: MS:1000507 ! ion attribute

[Term]
id: MS:1000234
name: mass resolving power
def: "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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000444 ! m/z Separation Method

[Term]
id: MS:1000235
name: total ion current chromatogram
def: "Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time." [PSI:MS]
synonym: "TIC chromatogram" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type

[Term]
id: MS:1000236
name: transmission
def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000496 ! instrument attribute

[Term]
id: MS:1000237
name: unified atomic mass unit
def: "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]
synonym: "u" EXACT []
is_obsolete: true

[Term]
id: MS:1000238
name: accelerator mass spectrometry
def: "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]
synonym: "AMS" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000239
name: atmospheric pressure matrix-assisted laser desorption ionization
def: "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]
synonym: "AP MALDI" EXACT []
is_a: MS:1000240 ! atmospheric pressure ionization

[Term]
id: MS:1000240
name: atmospheric pressure ionization
def: "Any ionization process in which ions are formed in the gas phase at atmospheric pressure." [PSI:MS]
synonym: "API" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000241
name: Atmostpheric Pressure Photoionization
def: "Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. OBSOLETE because redundant replace by MS:1000382 atmospheric pressure photoionization" [PSI:MS]
synonym: "APPI" EXACT []
is_obsolete: true

[Term]
id: MS:1000242
name: blackbody infrared radiative dissociation
def: "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]
synonym: "BIRD" EXACT []
is_a: MS:1000044 ! dissociation method
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000243
name: charge-remote fragmentation
def: "A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site." [PSI:MS]
synonym: "CRF" EXACT []
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000244
name: consecutive reaction monitoring
def: "MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS]
synonym: "CRM" EXACT []
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000245
name: charge stripping
def: "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]
synonym: "CS" EXACT []
is_a: MS:1000510 ! precursor activation attribute

[Term]
id: MS:1000246
name: delayed extraction
def: "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]
synonym: "DE" EXACT []
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000247
name: desorption ionization
def: "The formation of ions from a solid or liquid material after the rapid vaporization of that sample." [PSI:MS]
synonym: "DI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000248
name: direct insertion probe
def: "A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization." [PSI:MS]
synonym: "DIP" EXACT []
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000249
name: direct liquid introduction
def: "The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization." [PSI:MS]
synonym: "DLI" EXACT []
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000250
name: electron capture dissociation
def: "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]
synonym: "ECD" EXACT []
is_a: MS:1000044 ! dissociation method
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000251
name: even-electron ion
def: "An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state." [PSI:MS]
synonym: "EE" EXACT []
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000252
name: electron-induced excitation in organics
def: "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]
synonym: "EIEIO" EXACT []
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000253
name: electron multiplier
def: "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]
synonym: "EM" EXACT []
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000254
name: electrostatic energy analyzer
def: "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]
synonym: "ESA" EXACT []
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000255
name: flowing afterglow
def: "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]
synonym: "FA" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000256
name: high-field asymmetric waveform ion mobility spectrometry
def: "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]
synonym: "FAIMS" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000257
name: field desorption
def: "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]
synonym: "FD" EXACT []
is_a: MS:1000247 ! desorption ionization

[Term]
id: MS:1000258
name: field ionization
def: "The removal of electrons from any species by interaction with a high electric field." [PSI:MS]
synonym: "FI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000259
name: glow discharge ionization
def: "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]
synonym: "GD-MS" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000260
name: ion kinetic energy spectrometry
def: "A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge." [PSI:MS]
synonym: "IKES" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000261
name: ion mobility spectrometry
def: "The separation of ions according to their velocity through a buffer gas under the influence of an electric field." [PSI:MS]
synonym: "IMS" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000262
name: infrared multiphoton dissociation
def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS]
synonym: "IRMPD" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000263
name: isotope ratio mass spectrometry
def: "The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer." [PSI:MS]
synonym: "IRMS" EXACT []
is_a: MS:1000268 ! mass spectrometry

[Term]
id: MS:1000264
name: ion trap
def: "A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS]
synonym: "IT" EXACT []
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000265
name: kinetic energy release distribution
def: "Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction." [PSI:MS]
synonym: "KERD" EXACT []
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000266
name: Laser Desorption
alt_id: MS:1000394
def: "The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules. OBSOLETE as redudant, replace by laser desorption ionization MS:1000393" [PSI:MS]
synonym: "Laser Ionization MERGE" EXACT []
synonym: "LD" EXACT []
is_obsolete: true

[Term]
id: MS:1000267
name: mass analyzed ion kinetic energy spectrometry
def: "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]
synonym: "MIKES" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000268
name: mass spectrometry
def: "The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments." [PSI:MS]
synonym: "MS" EXACT []
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000269
name: mass spectrometry/mass spectrometry
def: "The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions." [PSI:MS]
synonym: "MS/MS" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000270
name: multiple stage mass spectrometry
def: "Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions." [PSI:MS]
synonym: "MSn" EXACT []
is_a: MS:1000445 ! sequential m/z separation method ?

[Term]
id: MS:1000271
name: Negative Ion chemical ionization
def: "Chemical ionization that results in the formation of negative ions." [PSI:MS]
synonym: "NICI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000272
name: neutralization reionization mass spectrometry
def: "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]
synonym: "NRMS" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000273
name: photoionization
def: "The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended." [PSI:MS]
synonym: "PI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000274
name: pyrolysis mass spectrometry
def: "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]
synonym: "PyMS" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000275
name: collision quadrupole
def: "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]
synonym: "q" EXACT []
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000276
name: resonance enhanced multiphoton ionization
def: "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]
synonym: "REMPI" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000277
name: residual gas analyzer
def: "A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber." [PSI:MS]
synonym: "RGA" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000278
name: surface enhanced laser desorption ionization
def: "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]
synonym: "SELDI" EXACT []
is_a: MS:1000406 ! surface ionization

[Term]
id: MS:1000279
name: surface enhanced neat desorption
def: "Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface." [PSI:MS]
synonym: "SEND" EXACT []
is_a: MS:1000406 ! surface ionization

[Term]
id: MS:1000280
name: suface ionization
def: "The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. OBSOLETE as redudant replace by  MS:1000406 surface ionization" [PSI:MS]
synonym: "SI" EXACT []
is_obsolete: true

[Term]
id: MS:1000281
name: selected ion flow tube
def: "A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions." [PSI:MS]
synonym: "SIFT" EXACT []
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000282
name: sustained off-resonance irradiation
def: "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]
synonym: "SORI" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000283
name: Spark Source Mass Spectrometry
def: "Mass spectrometry using spark ionization. OBSOLETE because redundant, replace by spark ionization MS:1000404." [PSI:MS]
synonym: "SSMS" EXACT []
is_obsolete: true

[Term]
id: MS:1000284
name: stored waveform inverse fourier transform
def: "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 MS/MS experiments." [PSI:MS]
synonym: "SWIFT" EXACT []
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000285
name: total ion current
def: "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]
synonym: "TIC" EXACT []
is_a: MS:1000499 ! spectrum attribute
xref: value-type:xsd\:float "The allowed value-type for this CV term."

[Term]
id: MS:1000286
name: time lag focusing
def: "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]
synonym: "TLF" EXACT []
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000287
name: time-of-flight mass spectrometer
def: "An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy." [PSI:MS]
synonym: "TOF-MS" EXACT []
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000288
name: cyclotron
def: "A device that uses an oscillating electric field and magnetic field to accelerate charged particles." [PSI:MS]
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000289
name: double-focusing mass spectrometer
def: "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]
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000290
name: hybrid mass spectrometer
def: "A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry." [PSI:MS]
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000291
name: linear ion trap
def: "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]
is_a: MS:1000264 ! ion trap

[Term]
id: MS:1000292
name: mass spectrograph obsolete
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000293
name: mass spectrometer
def: "An instrument that measures the mass-to-charge ratio and relative abundances of ions." [PSI:MS]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000294
name: mass spectrum
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000295
name: mattauch-herzog geometry
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000296
name: nier-johnson geometry
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000297
name: paul ion trap
def: "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]
synonym: "quadrupole ion trap" RELATED []
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000298
name: prolate traochoidal mass spectrometer
def: "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]
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000299
name: quistor
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000300
name: reflectron
def: "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]
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000301
name: sector mass spectrometer
def: "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]
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000302
name: tandem mass spectrometer
def: "A mass spectrometer designed for mass spectrometry/mass spectrometry." [PSI:MS]
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000303
name: transmission quadrupole mass spectrometer
def: "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]
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000304
name: accelerating voltage
def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000487 ! ion optics attribute
relationship: has_units UO:0000217 ! electric potential difference

[Term]
id: MS:1000305
name: cyclotron motion
def: "The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB." [PSI:MS]
is_a: MS:1000444 ! m/z Separation Method

[Term]
id: MS:1000306
name: dynamic mass spectrometry
def: "A mass spectrometer in which m/z separation using one or more electric fields that vary with time." [PSI:MS]
is_a: MS:1000293 ! mass spectrometer

[Term]
id: MS:1000307
name: einzel lens
def: "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]
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000308
name: electric field strength
def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS]
is_a: MS:1000487 ! ion optics attribute
xref: value-type:xsd\:float "The allowed value-type for this CV term."

[Term]
id: MS:1000309
name: first stability region
def: "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]
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000310
name: fringing field
def: "The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element." [PSI:MS]
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000311
name: kinetic energy analyzer
def: "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]
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000312
name: mass limit
def: "The m/z value above which ions cannot be detected in a mass spectrometer." [PSI:MS]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000313
name: scan m/z range?
def: "The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000314
name: mass selective axial ejection
def: "The use of mass selective instability to eject ions of selected m/z values from an ion trap." [PSI:MS]
is_a: MS:1000444 ! m/z Separation Method

[Term]
id: MS:1000315
name: mass selective instability
def: "A method for selective ejection of ions according to their m/z value in an ion trap." [PSI:MS]
is_a: MS:1000444 ! m/z Separation Method

[Term]
id: MS:1000316
name: mathieu stability diagram
def: "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]
is_a: MS:1000444 ! m/z Separation Method

[Term]
id: MS:1000317
name: orthogonal extraction
def: "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]
is_a: MS:1000444 ! m/z Separation Method

[Term]
id: MS:1000318
name: resonance ion ejection
def: "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]
is_a: MS:1000444 ! m/z Separation Method

[Term]
id: MS:1000319
name: space charge effect
def: "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]
is_a: MS:1000487 ! ion optics attribute

[Term]
id: MS:1000320
name: static field
def: "An electric or magnetic field that does not change in time." [PSI:MS]
is_a: MS:1000597 ! ion optics type

[Term]
id: MS:1000321
name: 2E Mass Spectrum
def: "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]
is_a: MS:1000445 ! sequential m/z separation method ?

[Term]
id: MS:1000322
name: charge inversion mass spectrum
def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS]
is_a: MS:1000294 ! mass spectrum

[Term]
id: MS:1000323
name: constant neutral loss scan
def: "A scan procedure for a tandem mass spectrometer designed to produce a constant neutral loss spectrum of different precursor ions by detection of the corresponding product ions produced by metastable ion fragmentation or collision-induced dissociation. Synonymous terms are constant neutral mass loss scan and fixed neutral fragment scan." [PSI:MS]
synonym: "constant neutral mass loss scan" RELATED []
synonym: "fixed neutral fragment scan" RELATED []
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000324
name: constant neutral gain scan
def: "Scan procedure for a tandem mass spectrometer designed to produce a constant neutral mass gain spectrum of different precursor ions by detection of the corresponding product ions of ion/molecule reactions with a gas in acollision cell." [PSI:MS]
synonym: "Constant Neutral Mass Gain Scan" EXACT []
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000325
name: constant neutral mass gain spectrum
def: "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]
is_a: MS:1000294 ! mass spectrum

[Term]
id: MS:1000326
name: constant neutral mass loss spectrum
def: "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]
synonym: "Constant Neutral Mass Loss" EXACT []
is_a: MS:1000294 ! mass spectrum

[Term]
id: MS:1000327
name: consecutive reaction monitoring
def: "A type of MS/MS experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. OBSOLETE as redundant replace by  consecutive reaction monitoring MS:1000244." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000328
name: e/2 mass spectrum
def: "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]
is_a: MS:1000294 ! mass spectrum

[Term]
id: MS:1000329
name: linked scan
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000330
name: linked scan at constant b/e
def: "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]
is_a: MS:1000329 ! linked scan

[Term]
id: MS:1000331
name: Linked Scan at Constant E2/V
def: "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]
is_a: MS:1000329 ! linked scan

[Term]
id: MS:1000332
name: Linked Scan at Constant B2/E
def: "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]
is_a: MS:1000329 ! linked scan

[Term]
id: MS:1000333
name: Linked Scan at Constant B[1-(E/E0)]^1/2 / E
def: "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]
is_a: MS:1000329 ! linked scan

[Term]
id: MS:1000334
name: MS/MS in Time
def: "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]
is_a: MS:1000445 ! sequential m/z separation method ?

[Term]
id: MS:1000335
name: MS/MS in Space
def: "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]
is_a: MS:1000445 ! sequential m/z separation method ?

[Term]
id: MS:1000336
name: neutral loss
def: "The loss of an uncharged species during a rearrangement process." [PSI:MS]
is_a: MS:1000445 ! sequential m/z separation method ?

[Term]
id: MS:1000337
name: nth generation product ion
def: "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]
synonym: "granddaughter ion" RELATED []
is_a: MS:1000342 ! product ion

[Term]
id: MS:1000338
name: nth generation product ion scan
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000339
name: nth generation product ion spectrum
def: "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]
is_a: MS:1000343 ! product ion spectrum

[Term]
id: MS:1000340
name: precursor ion
def: "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 not recommended." [PSI:MS]
synonym: "parent ion" RELATED []
is_a: MS:1000506 ! ion role

[Term]
id: MS:1000341
name: precursor ion spectrum
def: "The mass spectrum recorded from any spectrometer in which the appropriate m/z separation function can be set to record the precursor ion or ions of selected product ions." [PSI:MS]
is_a: MS:1000294 ! mass spectrum

[Term]
id: MS:1000342
name: product ion
def: "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]
synonym: "daughter ion" RELATED []
is_a: MS:1000506 ! ion role

[Term]
id: MS:1000343
name: product ion spectrum
def: "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]
is_a: MS:1000294 ! mass spectrum

[Term]
id: MS:1000344
name: progeny ion
def: "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]
synonym: "Progeny Fragment Ion" EXACT []
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000345
name: array detector
def: "Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector." [PSI:MS]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000346
name: conversion dynode
def: "A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected." [PSI:MS]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000347
name: dynode
def: "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]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000348
name: focal plane collector
def: "A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000349
name: ion-to-photon detector
def: "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]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000350
name: point collector
def: "A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially." [PSI:MS]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000351
name: postacceleration detector
def: "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]
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000352
name: secondary electron
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000353
name: adduct ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000354
name: aromatic ion
def: "A planar cyclic ion that obeys the Hckel (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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000355
name: analog ion
def: "Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+." [PSI:MS]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000356
name: anti-aromatic ion
def: "A planar cyclic ion with 4n ? electrons and is therefore not aromatic." [PSI:MS]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000357
name: cationized molecule
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000358
name: cluster ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000359
name: Conventional ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000360
name: diagnostic ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000361
name: dimeric ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000362
name: distonic ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000363
name: enium ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000364
name: fragment ion
def: "A product ion that results from the dissociation of a precursor ion. Replaced by MS:1000342- product ion." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000365
name: ion
def: "An atomic or molecular species having a net positive or negative electric charge." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000366
name: Isotopologue ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000367
name: Isotopomeric ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000368
name: metastable ion
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000369
name: molecular ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000370
name: negative ion
def: "An atomic or molecular species having a net negative electric charge." [PSI:MS]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000371
name: non-classical ion
def: "Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions." [PSI:MS]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000372
name: onium ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000373
name: principal ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000374
name: positive ion
def: "An atomic or molecular species having a net positive electric charge." [PSI:MS]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000375
name: protonated molecule
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000376
name: radical ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000377
name: reference ion
def: "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]
is_a: MS:1000508 ! ion chemical type

[Term]
id: MS:1000378
name: stable ion
def: "An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000379
name: unstable ion
def: "An ion with sufficient enerrgy to dissociate within the ion source." [PSI:MS]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000380
name: adiabatic ionization
def: "A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000381
name: associative ionization
def: "An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000382
name: atmospheric pressure photoionization
def: "Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS]
is_a: MS:1000240 ! atmospheric pressure ionization

[Term]
id: MS:1000383
name: autodetachment
def: "The formation of a neutral when a negative ion in a disrtete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000384
name: autoionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000385
name: charge exchange ionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000386
name: chemi-ionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000387
name: desorption/ionization on silicon
def: "The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface." [PSI:MS]
is_a: MS:1000247 ! desorption ionization

[Term]
id: MS:1000388
name: dissociative ionization
def: "The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000389
name: electron ionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000390
name: ion desolvation
def: "The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000391
name: ion-pair formation
def: "The reaction of a molecule to form both a positive ion and negative ion fragment among the products." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000392
name: ionization efficiency
def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute

[Term]
id: MS:1000393
name: laser desorption ionization
def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS]
is_a: MS:1000247 ! desorption ionization

[Term]
id: MS:1000395
name: liquid secondary ionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000396
name: membrane inlet
def: "A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source." [PSI:MS]
is_a: MS:1000007 ! inlet type

[Term]
id: MS:1000397
name: microelectrospray
def: "Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanaoelectrospray." [PSI:MS]
is_a: MS:1000073 ! electrospray ionization

[Term]
id: MS:1000398
name: nanoelectrospray
def: "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]
synonym: "nanospray" EXACT []
is_a: MS:1000073 ! electrospray ionization

[Term]
id: MS:1000399
name: penning ionization
def: "Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000400
name: plasma desorption ionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000401
name: pre-ionization state
def: "An electronic state capable of undergoing auto-Ionization." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000402
name: secondary ionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000403
name: soft ionization
def: "The formation of gas-phase ions without extensive fragmentation." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000404
name: spark ionization
def: "The formation of ions from a solid material by an intermittent electrical discharge." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000405
name: surface-assisted laser desorption ionization
def: "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]
is_a: MS:1000247 ! desorption ionization

[Term]
id: MS:1000406
name: surface ionization
def: "The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000407
name: thermal ionization
def: "The ionization of a neutral species through contact with a high temperature surface." [PSI:MS]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000408
name: vertical ionization
def: "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]
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000409
name: association reaction
def: "The reaction of an ion with a neutral species in which the reactants combine to form a single ion." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000410
name: alpha-cleavage
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000411
name: beta-cleavage
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000412
name: buffer gas
def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS]
is_a: MS:1000510 ! precursor activation attribute

[Term]
id: MS:1000413
name: charge-induced fragmentation
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000414
name: charge inversion reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000415
name: charge permutation reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000416
name: charge stripping reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000417
name: charge transfer reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000418
name: collisional excitation
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000419
name: collision gas
def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS]
is_a: MS:1000510 ! precursor activation attribute

[Term]
id: MS:1000420
name: heterolytic cleavage
def: "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]
synonym: "heterolysis" RELATED []
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000421
name: high energy collision
def: "Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000422
name: high-energy collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS]
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000423
name: homolytic cleavage
def: "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]
synonym: "homolysis" RELATED []
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000424
name: hydrogen/deuterium exchange
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000425
name: ion energy loss spectrum
def: "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]
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000426
name: ionizing collision
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000427
name: ion/molecule reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000428
name: ion/neutral complex
def: "A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000429
name: ion/neutral species reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000430
name: ion/neutral species exchange reaction
def: "In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000431
name: kinetic method
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000432
name: low energy collisions
def: "A collision between an ion and neutral species with translational energy approximately 1000 eV or lower." [PSI:MS]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000433
name: low-energy collision-induced dissociation
def: "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]
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000434
name: McLafferty Rearrangement
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000435
name: photodissociation
def: "A process wherein the reactant ion is dissociated as a result of absorption of one or more photons." [PSI:MS]
synonym: "Multiphoton Dissociation" EXACT []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1000436
name: partial charge transfer reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000437
name: ion reaction
def: "Chemical transformation involving an ion." [PSI:MS]
relationship: part_of MS:1000365 ! ion

[Term]
id: MS:1000438
name: superelastic collision
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000439
name: surface-induced reaction
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000440
name: unimolecular dissociation
def: "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]
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000441
name: scan
def: "Function or process of the mass spectrometer where it records a spectrum." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000442
name: spectrum
def: "A mass spectrum is an intensity vs m/z (mass-to-charge ratio) plot representing a chemical analysis." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000443
name: mass analyzer type
def: "Mass analyzer separates the ions according to their mass-to-charge ratio." [PSI:MS]
relationship: part_of MS:1000451 ! mass analyzer

[Term]
id: MS:1000444
name: m/z Separation Method
def: "TODO: Add definition." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000445
name: sequential m/z separation method ?
def: "TODO: Add definition." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000446
name: fast ion bombardment
def: "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]
synonym: "FIB" EXACT []
is_a: MS:1000008 ! ionization type

[Term]
id: MS:1000447
name: LTQ
def: "Finnigan LTQ MS." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000448
name: LTQ FT
def: "Finnigan LTQ FT MS." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000449
name: LTQ Orbitrap
def: "Finnigan LTQ Orbitrap MS." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000450
name: LXQ
def: "Finnigan LXQ MS." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000451
name: mass analyzer
def: "Terms used to describe the Analyzer." [PSI:MS]
relationship: part_of MS:1000463 ! instrument
synonym: "analyzer" EXACT []

[Term]
id: MS:1000452
name: data transformation
def: "Terms used to describe types of data processing." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
synonym: "data processing" EXACT []

[Term]
id: MS:1000453
name: detector
def: "The device that detects ions." [PSI:MS]
relationship: part_of MS:1000463 ! instrument

[Term]
id: MS:1000454
name: instrument additional description
def: "Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000455
name: ion selection attribute
def: "Ion selection properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1000456
name: precursor activation
def: "Terms to describe the precursor activation." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum
synonym: "activation" EXACT []

[Term]
id: MS:1000457
name: sample
def: "Terms to describe the sample." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000458
name: source
def: "Terms to describe the source." [PSI:MS]
relationship: part_of MS:1000463 ! instrument

[Term]
id: MS:1000459
name: spectrum instrument description
def: "Terms used to describe the spectrum." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000460
name: unit
def: "Terms to describe units." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000461
name: additional description
def: "Terms to describe Additional." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000462
name: ion optics
def: "Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions." [PSI:MS]
relationship: part_of MS:1000463 ! instrument

[Term]
id: MS:1000463
name: instrument
def: "Description of the instrument or the mass spectrometer." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
synonym: "instrument configuration" EXACT []

[Term]
id: MS:1000464
name: mass unit
def: "A unit of measurement for mass." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000465
name: scan polarity
def: "An acquisition mode to which specifies weather polarity is negative, positive or alternating." [PSI:MS]
relationship: part_of MS:1000441 ! scan

[Term]
id: MS:1000466
name: alternating
def: "Alternating." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000467
name: 1200 series LC/MSD SL
def: "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 MS/MS and 11 stages of manual MS/MS." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000468
name: 6110 Quadrupole LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000469
name: 6120 Quadrupole LC/MS
def: "The 6120 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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000470
name: 6130 Quadrupole LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000471
name: 6140 Quadrupole LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000472
name: 6210 Time-of-Flight LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000473
name: 6310 Ion Trap LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000474
name: 6320 Ion Trap LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000475
name: 6330 Ion Trap LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000476
name: 6340 Ion Trap LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000477
name: 6410 Triple Quadrupole LC/MS
def: "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]
synonym: "6410 Triple Quad LC/MS" EXACT []
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000478
name: 1200 series LC/MSD VL
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000479
name: purgatory
def: "Terms that will likely become obsolete unless there are wails of dissent." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000480
name: mass analyzer attribute
def: "Analyzer properties that are associated with a value." [PSI:MS]
relationship: part_of MS:1000451 ! mass analyzer

[Term]
id: MS:1000481
name: detector attribute
def: "Detector attribute recognized as a value." [PSI:MS]
relationship: part_of MS:1000453 ! detector

[Term]
id: MS:1000482
name: source attribute
def: "Property of a source device that need a value." [PSI:MS]
relationship: part_of MS:1000458 ! source

[Term]
id: MS:1000483
name: Thermo Fisher Scientific instrument model
def: "Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific." [PSI:MS]
synonym: "Thermo Scientific" RELATED []
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000484
name: orbitrap
def: "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]
is_a: MS:1000443 ! mass analyzer type

[Term]
id: MS:1000485
name: nanospray inlet
def: "Nanospray Inlet." [PSI:MS]
is_a: MS:1000057 ! electrospray inlet

[Term]
id: MS:1000486
name: source potential
def: "Potential difference at the MS source in volts." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000217 ! electric potential difference

[Term]
id: MS:1000487
name: ion optics attribute
def: "Ion optics involves components that help focus ion streams in mass spectrometry." [PSI:MS]
is_a: MS:1000462 ! ion optics

[Term]
id: MS:1000488
name: Hitachi instrument model
def: "Hitachi instrument model." [PSI:MS]
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000489
name: Varian instrument model
def: "Varian instrument model." [PSI:MS]
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000490
name: Agilent instrument model
def: "Agilent instrument model." [PSI:MS]
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000491
name: Dionex instrument model
def: "Dionex instrument model." [PSI:MS]
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000492
name: Thermo Electron instrument model
def: "Thermo Electron Corporation instrument model." [PSI:MS]
is_a: MS:1000483 ! Thermo Fisher Scientific instrument model

[Term]
id: MS:1000493
name: Finnigan MAT instrument model
def: "Finnigan MAT instrument model." [PSI:MS]
is_a: MS:1000483 ! Thermo Fisher Scientific instrument model

[Term]
id: MS:1000494
name: Thermo Scientific instrument model
def: "Thermo Scientific instrument model." [PSI:MS]
is_a: MS:1000483 ! Thermo Fisher Scientific instrument model

[Term]
id: MS:1000495
name: Applied Biosystems instrument model
def: "Applied Biosystems instrument model." [PSI:MS]
synonym: "ABI" EXACT []
is_a: MS:1000031 ! instrument model

[Term]
id: MS:1000496
name: instrument attribute
def: "Instrument properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000463 ! instrument

[Term]
id: MS:1000497
name: zoom scan
def: "Feature of the ion trap mass spectrometer where MSMS data is acquired over a certain mass range." [PSI:MS]
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000498
name: full scan
def: "Feature of the ion trap mass spectrometer where MS data is acquired over a mass range." [PSI:MS]
is_a: MS:1000020 ! scanning method

[Term]
id: MS:1000499
name: spectrum attribute
def: "Spectrum properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1000500
name: scan m/z upper limit
def: "The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "mzRangeStop" RELATED []
is_a: MS:1000549 ! selection window attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000501
name: scan m/z lower limit
def: "The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "mzRangeStart" RELATED []
is_a: MS:1000549 ! selection window attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000502
name: dwell time
def: "The time spent gathering data across a peak." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "Scan Duration" RELATED []
is_a: MS:1000549 ! selection window attribute
relationship: has_units UO:0000003 ! time unit

[Term]
id: MS:1000503
name: scan attribute
def: "Scan properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000441 ! scan

[Term]
id: MS:1000504
name: base peak m/z
def: "M/z value of the greatest peak in the mass spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000505
name: base peak intensity
def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1000506
name: ion role
def: "Ion Role." [PSI:MS]
relationship: part_of MS:1000365 ! ion

[Term]
id: MS:1000507
name: ion attribute
def: "Ion properties that are associated with a value." [PSI:MS]
relationship: part_of MS:1000365 ! ion

[Term]
id: MS:1000508
name: ion chemical type
def: "Ion Type." [PSI:MS]
relationship: part_of MS:1000365 ! ion

[Term]
id: MS:1000509
name: activation energy
def: "Activation Energy." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000111 ! energy unit

[Term]
id: MS:1000510
name: precursor activation attribute
def: "Precursor Activation Attribute." [PSI:MS]
relationship: part_of MS:1000456 ! precursor activation

[Term]
id: MS:1000511
name: ms level
def: "Stages of ms achieved in a multi stage mass spectrometry experiment." [PSI:MS]
xref: value-type:xsd\:int"The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1000512
name: filter string
def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1000513
name: binary data array
def: "A data array of values." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum
relationship: part_of MS:1000625 ! chromatogram

[Term]
id: MS:1000514
name: m/z array
def: "A data array of mass divided by charge values." [PSI:MS]
is_a: MS:1000513 ! binary data array
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000515
name: intensity array
def: "A data array of intensity values." [PSI:MS]
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1000516
name: charge array
def: "A data array of charge values." [PSI:MS]
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1000517
name: signal to noise array
def: "A data array of signal-to-noise values." [PSI:MS]
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1000518
name: binary data type
def: "Binary Data type. 16-bit integer, 32-bit integer, 32-bit float 64-bit integer 64-bit float." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum
relationship: part_of MS:1000625 ! chromatogram

[Term]
id: MS:1000519
name: 32-bit integer
def: "Signed 32-bit integer." [PSI:MS]
is_a: MS:1000518 ! binary data type

[Term]
id: MS:1000520
name: 16-bit float
def: "Signed 16-bit float." [PSI:MS]
is_a: MS:1000518 ! binary data type

[Term]
id: MS:1000521
name: 32-bit float
def: "Signed 32-bit float. IEEE-754." [PSI:MS]
is_a: MS:1000518 ! binary data type

[Term]
id: MS:1000522
name: 64-bit integer
def: "Signed 64-bit integer." [PSI:MS]
is_a: MS:1000518 ! binary data type

[Term]
id: MS:1000523
name: 64-bit float
def: "Signed 64-bit float. IEEE-754." [PSI:MS]
is_a: MS:1000518 ! binary data type

[Term]
id: MS:1000524
name: data file content
def: "Describes the data content on the file." [PSI:MS]
relationship: part_of MS:1000577 ! data file

[Term]
id: MS:1000525
name: spectrum representation
def: "Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1000526
name: MassLynx raw format
def: "MassLynx raw file format, which is actually a directory/folder containing several files for each ms run." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000527
name: highest m/z value
def: "Highest m/z value observed in the mass spectum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000528
name: lowest m/z value
def: "Lowest m/z value observed in the mass spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000529
name: instrument serial number
def: "Serial Number of the instrument." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000496 ! instrument attribute

[Term]
id: MS:1000530
name: file format conversion
def: "Conversion of one file format to another." [PSI:MS]
is_a: MS:1000452 ! data transformation

[Term]
id: MS:1000531
name: software
def: "Software related to the recording or transformation of spectra." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000532
name: Xcalibur
def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000693 ! Thermo Finnigan software

[Term]
id: MS:1000533
name: Bioworks
def: "Thermo Finnigan software for data analysis of peptides and proteins." [PSI:MS]
synonym: "Bioworks Browser" RELATED []
is_a: MS:1000693 ! Thermo Finnigan software

[Term]
id: MS:1000534
name: Masslynx
def: "Miromass software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000535
name: FlexAnalysis
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000536
name: data explorer
def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000691 ! Applied Biosystems software

[Term]
id: MS:1000537
name: 4700 Explorer
def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000691 ! Applied Biosystems software

[Term]
id: MS:1000538
name: massWolf
def: "A software for converting Waters raw directory format to mzXML or mzML. massWolf was originally developed at the Institute for Systems Biology." [PSI:MS]
is_a: MS:1000531 ! software
synonym: "wolf" EXACT []

[Term]
id: MS:1000539
name: Voyager Biospectrometry Workstation System
def: "Applied Biosystems MALDI-TOF data acquisition and analysis system." [PSI:MS]
is_a: MS:1000691 ! Applied Biosystems software

[Term]
id: MS:1000540
name: FlexControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000541
name: ReAdW
def: "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]
is_a: MS:1000531 ! software

[Term]
id: MS:1000542
name: MzStar
def: "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]
is_a: MS:1000531 ! software

[Term]
id: MS:1000543
name: data processing action
def: "Data processing attribute used to describe the type of data processing performed on the data file." [PSI:MS]
is_a: MS:1000452 ! data transformation

[Term]
id: MS:1000544
name: Conversion to mzML
def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS]
is_a: MS:1000530 ! file format conversion

[Term]
id: MS:1000545
name: Conversion to mzXML
def: "Conversion of a file format to Institute of Systems Biology mzXML file format." [PSI:MS]
is_a: MS:1000530 ! file format conversion

[Term]
id: MS:1000546
name: Conversion to mzData
def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS]
is_a: MS:1000530 ! file format conversion

[Term]
id: MS:1000547
name: object attribute
def: "Object Attribute." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000548
name: sample attribute
def: "Sample properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000457 ! sample

[Term]
id: MS:1000549
name: selection window attribute
def: "Selection window properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000441 ! scan

[Term]
id: MS:1000550
name: time unit
def: "Time Unit." [PSI:MS]
is_obsolete: true

[Term]
id: MS:1000551
name: Analyst
def: "AB SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000552
name: maldi spot identifier
def: "Maldi Spot Identifier." [PSI:MS]
relationship: part_of MS:1000479 ! purgatory

[Term]
id: MS:1000553
name: Trapper
def: "A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000554
name: LCQ Deca
def: "ThermoFinnigan LCQ Deca." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000555
name: LTQ Orbitrap Discovery
def: "LTQ Orbitrap Discovery." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000556
name: LTQ Orbitrap XL
def: "LTQ Orbitrap XL." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000557
name: LTQ FT Ultra
def: "LTQ FT Ultra." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000558
name: GC Quantum
def: "GC Quantum." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000559
name: spectrum type
def: "Spectrum type." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1000560
name: source file type
def: "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]
relationship: part_of MS:1000577 ! data file

[Term]
id: MS:1000561
name: data file checksum type
def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS]
relationship: part_of MS:1000577 ! data file

[Term]
id: MS:1000562
name: wiff file
def: "Applied Biosystems wiff file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000563
name: Xcalibur RAW file
def: "Thermo Finnigan RAW file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000564
name: mzData file
def: "Proteomics Standards Inititative mzData file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000565
name: pkl file
def: "Micromass pkl file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000566
name: mzXML file
def: "Institute of Systems Biology mzXML file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000567
name: yep file
def: "Bruker yep file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000568
name: MD5
def: "MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS]
is_a: MS:1000561 ! data file checksum type
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000569
name: SHA-1
def: "SHA-1 (Secure Hash Algorithm-1) 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]
is_a: MS:1000561 ! data file checksum type
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000570
name: spectra combination
def: "Method used to combine the mass spectra." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1000571
name: sum of spectra
def: "Spectra Sum." [PSI:MS]
is_a: MS:1000570 ! spectra combination

[Term]
id: MS:1000572
name: binary data compression type
def: "Compression Type." [PSI:MS]
relationship: part_of MS:1000442 ! spectrum
relationship: part_of MS:1000625 ! chromatogram

[Term]
id: MS:1000573
name: median of spectra
def: "Spectra is combined by calculating the median of the spectra." [PSI:MS]
is_a: MS:1000570 ! spectra combination

[Term]
id: MS:1000574
name: zlib compression
def: "Zlib." [PSI:MS]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1000575
name: mean of spectra
def: "Spectra is combined by calculating the mean of the spectra." [PSI:MS]
is_a: MS:1000570 ! spectra combination

[Term]
id: MS:1000576
name: no compression
def: "No Compression." [PSI:MS]
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1000577
name: data file
def: "Describes the type of file and its content." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology
synonym: "source file" EXACT []

[Term]
id: MS:1000578
name: LCQ Fleet
def: "LCQ Fleet." [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000579
name: MS1 spectrum
def: "MS1 refers to single-stage MS/MS experiments designed to record the first stage of the product ion spectra." [PSI:MS]
synonym: "Single-Stage Mass Spectrometry" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000580
name: MSn spectrum
def: "MSn refers to multi-stage MS/MS 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." [PSI:MS]
synonym: "multiple-stage mass spectrometry spectrum" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000581
name: CRM spectrum
def: "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]
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000582
name: SIM spectrum
def: "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]
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000583
name: SRM spectrum
def: "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]
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000584
name: mzML file
def: "Proteomics Standards Inititative mzML file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000585
name: contact person attribute
def: "Details about a person to contact in case of concern or dicussion about the file." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000577 ! data file

[Term]
id: MS:1000586
name: contact name
def: "Name of a contact person." [PSI:MS]
is_a: MS:1000585 ! contact person attribute
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000587
name: contact address
def: "Postal address of a contact person." [PSI:MS]
is_a: MS:1000585 ! contact person attribute
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000588
name: contact URL
def: "Uniform Resource Locator related to the contact person." [PSI:MS]
is_a: MS:1000585 ! contact person attribute
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000589
name: contact email
def: "Email adress of the contact person." [PSI:MS]
is_a: MS:1000585 ! contact person attribute
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000590
name: contact organization
def: "Home institution of the contact person." [PSI:MS]
is_a: MS:1000585 ! contact person attribute
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000591
name: MzWiff
def: "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]
is_a: MS:1000531 ! software

[Term]
id: MS:1000592
name: smoothing
def: "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]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000593
name: baseline reduction
def: "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]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000594
name: low intensity data point removal
def: "The removal of very low intensity data points that are likely to be spurious noise rather than real signal." [PSI:MS]
synonym: "thresholding" EXACT []
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000595
name: time array
def: "A data array of relative time offset values from a reference time." [PSI:MS]
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000003 ! time unit

[Term]
id: MS:1000596
name: measurement method
def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000597
name: ion optics type
def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS]
is_a: MS:1000462 ! ion optics

[Term]
id: MS:1000598
name: electron transfer dissociation
def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them." [PSI:MS]
synonym: "ETD" EXACT []
is_a: MS:1000044 ! dissociation method
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000599
name: pulsed q dissociation
def: "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]
synonym: "PQD" EXACT []
is_a: MS:1000044 ! dissociation method
is_a: MS:1000437 ! ion reaction

[Term]
id: MS:1000600
name: Proteios
def: "Database application and analysis platform for proteomics." [PSI:MS, source:www.proteios.org]
is_a: MS:1000531 ! software

[Term]
id: MS:1000601
name: ProteinLynx Global Server
def: "Waters software for data analysis." [PSI:MS]
is_a: MS:1000694 ! Waters software

[Term]
id: MS:1000602
name: Shimadzu Biotech instrument model
def: "Shimadzu Biotech instrument model." [PSI:MS]
is_a: MS:1000124 ! Shimadzu instrument model

[Term]
id: MS:1000603
name: Shimadzu Scientific Instruments instrument model
def: "Shimadzu Scientific Instruments instrument model." [PSI:MS]
is_a: MS:1000124 ! Shimadzu instrument model

[Term]
id: MS:1000604
name: LCMS-IT-TOF
def: "Shimadzu Scientific Instruments LCMS-IT-TOF MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1000605
name: LCMS-2010EV
def: "Shimadzu Scientific Instruments LCMS-2010EV MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1000606
name: LCMS-2010A
def: "Shimadzu Scientific Instruments LCMS-2010A MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1000607
name: AXIMA CFR MALDI-TOF
def: "Shimadzu Biotech AXIMA CFR MALDI-TOF MS." [PSI:MS]
is_a: MS:1000602 ! Shimadzu Biotech instrument model

[Term]
id: MS:1000608
name: AXIMA-QIT
def: "Shimadzu Biotech AXIMA-QIT MS." [PSI:MS]
is_a: MS:1000602 ! Shimadzu Biotech instrument model

[Term]
id: MS:1000609
name: AXIMA-CFR plus
def: "Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS]
is_a: MS:1000602 ! Shimadzu Biotech instrument model

[Term]
id: MS:1000610
name: AXIMA Performance MALDI-TOF/TOF
def: "Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS." [PSI:MS]
is_a: MS:1000602 ! Shimadzu Biotech instrument model

[Term]
id: MS:1000611
name: AXIMA Confidence MALDI-TOF
def: "Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS." [PSI:MS]
is_a: MS:1000602 ! Shimadzu Biotech instrument model

[Term]
id: MS:1000612
name: AXIMA Assurance Linear MALDI-TOF
def: "Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS." [PSI:MS]
is_a: MS:1000602 ! Shimadzu Biotech instrument model

[Term]
id: MS:1000613
name: dta file
def: "Peak list file format that should be better defined FIXME." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000614
name: ProteinLynx Global Server mass spectrum XML file
def: "Peak list file format used by ProteinLynx Global Server." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000615
name: ProteoWizard
def: "ProteoWizard software for data analysis. Currently developed and maintained by Darren Kessner at Parag Mallick's lab SFCAP at Cedars-Sinai." [PSI:MS]
synonym: "pwiz" EXACT []
is_a: MS:1000531 ! software

[Term]
id: MS:1000616
name: preset scan configuration
def: "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]
is_a: MS:1000503 ! scan attribute
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: MS:1000617
name: wavelength array
def: "A data array of electromagnetic radiation wavelength values." [PSI:MS]
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1000618
name: highest wavelength value
def: "Highest wavelength value observed in the uv/vis spectum." [PSI:MS]
is_a: MS:1000499 ! spectrum attribute
xref: value-type:xsd\:float "The allowed value-type for this CV term."

[Term]
id: MS:1000619
name: lowest wavelength value
def: "Lowest wavelength value observed in the uv/vis spectrum." [PSI:MS]
is_a: MS:1000499 ! spectrum attribute
xref: value-type:xsd\:float "The allowed value-type for this CV term."

[Term]
id: MS:1000620
name: PDA spectrum
def: "Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000621
name: photodiode array detector
def: "An array detector used to record spectra in the ultraviolet and visable region of light." [PSI:MS]
synonym: "PDA" EXACT []
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000622
name: Surveyor PDA
def: "Surveyor PDA." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000623
name: Accela PDA
def: "Accela PDA." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000624
name: inductive detector
def: "Inductive detector." [PSI:MS]
synonym: "image current detector" EXACT []
is_a: MS:1000026 ! detector type

[Term]
id: MS:1000625
name: chromatogram
def: "The representation of detector response versus time." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology

[Term]
id: MS:1000626
name: chromatogram type
def: "Broad category or type of a chromatogram." [PSI:MS]
relationship: part_of MS:1000625 ! chromatogram

[Term]
id: MS:1000627
name: selected ion current chromatogram
def: "Chromatogram created by creating an array of the measurements of a specific single ion current at each time point." [PSI:MS]
synonym: "SIC chromatogram" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type
is_a: MS:1000626 ! chromatogram type

[Term]
id: MS:1000628
name: basepeak chromatogram
def: "Chromatogram created by creating an array of the most intense peaks at each time point." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type

[Term]
id: MS:1000629
name: low intensity threshold
def: "Threshold below which some action is taken." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

[Term]
id: MS:1000630
name: data processing parameter
def: "Data processing parameter used in the data processing performed on the data file." [PSI:MS]
is_a: MS:1000452 ! data transformation

[Term]
id: MS:1000631
name: high intensity threshold
def: "Threshold above which some action is taken." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

[Term]
id: MS:1000632
name: Q-Tof Premier
def: "Waters Q-Tof Premier MS." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000633
name: possible charge state
def: "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]
xref: value-type:xsd\:int" The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute

[Term]
id: MS:1000634
name: DSQ
def: "ThermoFinnigan DSQ GC-MS" [PSI:MS]
is_a: MS:1000125 ! Thermo Finnigan instrument model

[Term]
id: MS:1000635
name: ITQ 700
def: "Thermo Scientific ITQ 700 GC-MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000636
name: ITQ 900
def: "Thermo Scientific ITQ 900 GC-MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000637
name: ITQ 1100
def: "Thermo Scientific ITQ 1100 GC-MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000638
name: LTQ XL ETD
def: "Thermo Scientific LTQ XL MS with ETD" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000639
name: LTQ Orbitrap XL ETD
def: "Thermo Scientific LTQ Orbitrap XL MS with ETD" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000640
name: DFS
def: "Thermo Scientific DFS HR GC-MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000641
name: DSQ II
def: "Thermo Scientific DSQ II GC-MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000642
name: MALDI LTQ XL
def: "Thermo Scientific MALDI LTQ XL MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000643
name: MALDI LTQ Orbitrap
def: "Thermo Scientific MALDI LTQ Orbitrap MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000644
name: TSQ Quantum Access
def: "Thermo Scientific TSQ Quantum Access MS." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000645
name: Element XR
def: "Thermo Scientific Element XR HR-ICP-MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000646
name: Element 2
def: "Thermo Scientific Element 2 HR-ICP-MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000647
name: Element GD
def: "Thermo Scientific Element GD Glow Discharge MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000648
name: GC IsoLink
def: "Thermo Scientific GC IsoLink Isotope Ratio MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000649
name: Exactive
def: "Thermo Scientific Exactive MS" [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000650
name: Proteomics Discoverer
def: "Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS]
is_a: MS:1000693 ! Thermo Finnigan software

[Term]
id: MS:1000651
name: 3200 QTRAP
def: "AB SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200" [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000652
name: 4800 Plus MALDI TOF-TOF Analyzer
def: "AB SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer" [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000653
name: API 3200
def: "AB SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000654
name: API 5000
def: "AB SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000655
name: QSTAR Elite
def: "AB SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite" [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000656
name: QSTAR Pulsar
def: "Applied Biosystems|MDS SCIEX QSTAR Pulsar" [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000657
name: QSTAR XL
def: "Applied Biosystems|MDS SCIEX QSTAR XL" [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000658
name: 4800 Proteomics Analyzer
def: "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer" [PSI:MS]
is_a: MS:1000495 ! Applied Biosystems instrument model

[Term]
id: MS:1000659
name: 4000 Series Explorer Software
def: "AB SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000661
name: GPS Explorer
def: "AB SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000662
name: LightSight Software
def: "AB SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000663
name: ProteinPilot Software
def: "AB SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000664
name: TissueView Software
def: "Applied Biosystems|MDS SCIEX software for tissue imaging." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000665
name: MarkerView Software
def: "Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000666
name: MRMPilot Software
def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000667
name: BioAnalyst
def: "Applied Biosystems|MDS SCIEX software for bio-related data exploration." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000668
name: Pro ID
def: "Applied Biosystems|MDS SCIEX software for protein identification." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000669
name: Pro ICAT
def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000670
name: Pro Quant
def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000671
name: Pro BLAST
def: "Applied Biosystems|MDS SCIEX software for MS-BLAST identification." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000672
name: Cliquid?
def: "AB SCIEX or Applied Biosystems software." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000673
name: MIDAS Workflow Designer
def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000674
name: MultiQuant
def: "Applied Biosystems|MDS SCIEX software for MRM-based quantitation." [PSI:MS]
is_a: MS:1000690 ! AB SCIEX software

[Term]
id: MS:1000675
name: 6220 Time-of-Flight LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000676
name: 6510 Quadrupole Time-of-Flight LC/MS
def: "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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000677
name: 6520 Quadrupole Time-of-Flight LC/MS
def: "The 6520 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]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1000678
name: MassHunter Data Acquisition
def: "Software for data acquisition of 6000 series instruments." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000679
name: MassHunter Easy Access
def: "Software for open access data acquisition." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000680
name: MassHunter Qualitative Analysis
def: "Software for data analysis of data from 6000 series instruments." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000681
name: MassHunter Quantitative Analysis
def: "Software for quantitation of Triple Quadruople and Quadrupole Time-of-Flight data." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000682
name: MassHunter Metabolite ID
def: "Software for identification of metabolites." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000683
name: MassHunter BioConfirm
def: "Software for protein characterization." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000684
name: Genespring MS
def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000685
name: MassHunter Mass Profiler
def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000686
name: METLIN
def: "Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000687
name: Spectrum Mill for MassHunter Workstation
def: "Software for protein identification and characterization of complex protein digest mixtures." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000688
name: 6300 Series Ion Trap Data Analysis Software
def: "Software for data analysis of 6300 series ion trap mass spectrometers." [PSI:MS]
is_a: MS:1000689 ! Agilent software

[Term]
id: MS:1000689
name: Agilent software
def: "Agilent software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000690
name: AB SCIEX software
def: "AB SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000691
name: Applied Biosystems software
def: "Applied Biosystems|MDS SCIEX software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000692
name: Bruker software
def: "Bruker software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000693
name: Thermo Finnigan software
def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS]
synonym: "Bioworks Browser" RELATED []
is_a: MS:1000531 ! software

[Term]
id: MS:1000694
name: Waters software
def: "Waters software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000695
name: apex ultra
def: "Bruker Daltonics apex ultra" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000696
name: autoflex III smartbeam
def: "Bruker Daltonics autoflex III smartbeam" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000697
name: HCT Series
def: "Bruker Daltonics HCT Series" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000698
name: HCTultra
def: "Bruker Daltonics HCTultra" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000699
name: HCTultra PTM
def: "Bruker Daltonics HCTultra PTM Discovery System" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000700
name: HCTultra ETD II
def: "Bruker Daltonics HCTultra ETD II System" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000701
name: microflex LT
def: "Bruker Daltonics microflex MS." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000702
name: micrOTOF
def: "Bruker Daltonics micrOTOF" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000703
name: micrOTOF-Q
def: "Bruker Daltonics micrOTOF-Q" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000704
name: micrOTOF-Q II
def: "Bruker Daltonics micrOTOF-Q II" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000705
name: ultraflex III TOF/TOF
def: "Bruker Daltonics ultraflex III TOF/TOF" [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1000706
name: apexControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000707
name: BioTools
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000708
name: CLINPROT
def: "Bruker CLINPROT software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000709
name: CLINPROT micro
def: "Bruker CLINPROT micro software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000710
name: CLINPROT robot
def: "Bruker CLINPROT robot software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000711
name: ClinProTools
def: "Bruker ClinProTools software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000712
name: Compass
def: "Bruker Compass software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000713
name: Compass for HCT/esquire
def: "Bruker Compass for HCT/esquire software" [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000714
name: Compass for micrOTOF
def: "Bruker Compass for micrOTOF software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000715
name: Compass OpenAccess
def: "Bruker compass OpenAccess software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000716
name: Compass Security Pack
def: "Bruker compass Security Pack software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000717
name: CompassXport
def: "Bruker stand-alone software for data conversion." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000718
name: CompassXtract
def: "Bruker software library for data access." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000719
name: DataAnalysis
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000720
name: dpControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000721
name: esquireControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000722
name: flexImaging
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000723
name: GENOLINK
def: "Bruker GENOLINK software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000724
name: GenoTools
def: "Bruker GenoTools software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000725
name: HCTcontrol
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000726
name: micrOTOFcontrol
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000727
name: PolyTools
def: "Bruker PolyTools software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000728
name: ProfileAnalysis
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000729
name: PROTEINEER
def: "Bruker PROTEINEER software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000730
name: PROTEINEER dp
def: "Bruker PROTEINEER dp software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000731
name: PROTEINEER fc
def: "Bruker PROTEINEER fc software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000732
name: PROTEINEER spII
def: "Bruker PROTEINEER spII software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000733
name: PROTEINEER-LC
def: "Bruker PROTEINEER-LC software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000734
name: ProteinScape
def: "Bruker ProteinScape software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000735
name: PureDisk
def: "BrukerPureDisk software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000736
name: QuantAnalysis
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000737
name: spControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000738
name: TargetAnalysis
def: "Bruker TargetAnalysis software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000739
name: WARP-LC
def: "Bruker WARP-LC software." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000740
name: parameter file
def: "Parameter file used to configure the acquisition of raw data on the instrument." [PSI:MS]
is_a: MS:1000560 ! Source File Type

[Term]
id: MS:1000741
name: Conversion to dta
def: "Conversion to dta format." [PSI:MS]
is_a: MS:1000530 ! file format conversion

[Term]
id: MS:1000742
name: Bioworks SRF file
def: "Thermo Finnigan SRF file format." [PSI:MS]
is_a: MS:1000560 ! source file type

[Term]
id: MS:1000743
name: TSQ Quantum Ultra AM
def: "Thermo Scientific TSQ Quantum Ultra AM." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000744
name: selected m/z
def: "Mass-to-charge ratio of the ion selected for fragmentation" [PSI:MS]
is_a: MS:1000455 ! ion selection attribute
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000745
name: retention time alignment
def: "The correction of the spectrum scan times, as used e.g. in label-free proteomics." [PSI:MS]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000746
name: high intensity data point removal
def: "The removal of very high intensity data points." [PSI:MS]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000747
name: completion time
def: "The time that a data processing action was finished." [PSI:MS]
is_a: MS:1000630 ! data processing parameter
xref: value-type:xsd\:date "The allowed value-type for this CV term."

[Term]
id: MS:1000748
name: SSQ 7000
def: "ThermoFinnigan SSQ 7000 MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000749
name: TSQ 7000
def: "ThermoFinnigan TSQ 7000 MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000750
name: TSQ
def: "ThermoFinnigan TSQ MS." [PSI:MS]
is_a: MS:1000493 ! Finnigan MAT instrument model

[Term]
id: MS:1000751
name: TSQ Quantum Ultra
def: "Thermo Scientific TSQ Quantum Ultra." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000752
name: TOPP software
def: "TOPP (The OpenMS proteomics pipeline) software." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000753
name: BaselineFilter
def: "Removes the baseline from profile spectra using a top-hat filter." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000754
name: DBExporter
def: "Exports data from an OpenMS database to a file." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000755
name: DBImporter
def: "Imports data to an OpenMS database." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000756
name: FileConverter
def: "Converts between different MS file formats." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000757
name: FileFilter
def: "Extracts or manipulates portions of data from peak, feature or consensus feature files." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000758
name: FileMerger
def: "Merges several MS files into one file." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000759
name: InternalCalibration
def: "Applies an internal calibration." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000760
name: MapAligner
def: "Corrects retention time distortions between maps." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000761
name: MapNormalizer
def: "Normalizes peak intensities in an MS run." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000762
name: NoiseFilter
def: "Removes noise from profile spectra by using different smoothing techniques." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000763
name: PeakPicker
def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000764
name: Resampler
def: "Transforms an LC/MS map into a resampled map or a png image." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000765
name: SpectraFilter
def: "Applies a filter to peak spectra." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000766
name: TOFCalibration
def: "Applies time of flight calibration." [PSI:MS]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1000767
name: native spectrum identifier format
def: "Describes how the native spectrum identifiers are formated." [PSI:MS]
synonym: "nativeID format" EXACT []
relationship: part_of MS:1000577 ! data file

[Term]
id: MS:1000768
name: Thermo nativeID format
def: "controller=xsd:nonNegativeInteger scan=xsd:positiveInteger." [PSI:MS]
comment: controller=0 is usually the mass spectrometer
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000769
name: Waters nativeID format
def: "function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000770
name: WIFF nativeID format
def: "sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000771
name: Bruker/Agilent YEP nativeID format
def: "scan=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000772
name: Bruker BAF nativeID format
def: "scan=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000773
name: Bruker FID nativeID format
def: "file=xsd:IDREF" [PSI:MS]
comment: The nativeID must be the same as the source file ID.
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000774
name: multiple peak list nativeID format
def: "index=xsd:nonNegativeInteger" [PSI:MS]
comment: 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.
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000775
name: single peak list nativeID format
def: "file=xsd:IDREF" [PSI:MS]
comment: 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.
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000776
name: scan number only nativeID format
def: "scan=xsd:nonNegativeInteger" [PSI:MS]
comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000777
name: spectrum identifier nativeID format
def: "spectrum=xsd:nonNegativeInteger" [PSI:MS]
comment: Used for conversion from mzData. The spectrum id attribute is referenced.
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000778
name: charge state calculation
def: "A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm." [PSI:MS]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000779
name: below precursor intensity dominance charge state calculation
def: "Infers charge state as single or amibiguously multiple by determining the fraction of intensity below the precursor m/z." [PSI:MS]
is_a: MS:1000778 ! charge state calculation

[Term]
id: MS:1000780
name: precursor recalculation
def: "A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions." [PSI:MS]
is_a: MS:1000543 ! data processing action

[Term]
id: MS:1000781
name: msPrefix precursor recalculation
def: "Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans." [PSI:MS]
is_a: MS:1000780 ! precursor recalculation

[Term]
id: MS:1000782
name: Savitzky-Golay smoothing
def: "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]
is_a: MS:1000592 ! smoothing

[Term]
id: MS:1000783
name: LOWESS smoothing
def: "Reduces intensity spikes by applying a modeling 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]
is_a: MS:1000592 ! smoothing

[Term]
id: MS:1000784
name: Gaussian smoothing
def: "Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function." [PSI:MS]
synonym: "Weierstrass transform" EXACT []
synonym: "binomial smoothing" EXACT []
is_a: MS:1000592 ! smoothing

[Term]
id: MS:1000785
name: moving average smoothing
def: "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]
synonym: "box smoothing" EXACT []
synonym: "boxcar smoothing" EXACT []
synonym: "sliding average smoothing" EXACT []
is_a: MS:1000592 ! smoothing

[Typedef]
id: has_units
name: has_units

[Typedef]
id: part_of
name: part_of
is_transitive: true

