/usr/lib/python2.7/dist-packages/pymzml/obo/psi-ms-2.6.0.obo

format-version: 1.2
date: 30:04:2009 11:14
saved-by: edeutsch
auto-generated-by: OBO-Edit 1.101
default-namespace: MS
remark: namespace: MS
remark: version: 2.6.0
remark: release date: 2009-05-22
remark: coverage: Mass spectrometer output files and spectra interpretation
remark: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>, Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de> 
remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics 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: import: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo?revision=1.20

[Term]
id: MS:0000000
name: Proteomics Standards Initiative Mass Spectrometry Vocabularies
def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [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]
is_a: MS:1000548 ! sample attribute

[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:0000021 ! gram

[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:0000098 ! milliliter

[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:0000175 ! gram per liter

[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: "OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer." [PSI:MS]
comment: This term was made obsolete because it was replaced by scan polarity (MS:1000465)
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: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute

[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 MS:1000040 ! m/z
relationship: has_units UO:0000169 ! parts per million

[Term]
id: MS:1000015
name: scan rate
def: "Rate in Th/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
relationship: has_units MS:1000807 ! Th/s

[Term]
id: MS:1000016
name: scan start time
def: "The time that an analyzer started a scan, relative to the start of the MS 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:0000010 ! second
relationship: has_units UO:0000031 ! minute

[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:1000479 ! purgatory

[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:0000008 ! meter

[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:1000479 ! purgatory
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]
synonym: "B" EXACT []
synonym: "Magnetic Field" RELATED []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000480 ! mass analyzer attribute
relationship: has_units UO:0000228 ! tesla

[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]
synonym: "ADC Sampling Frequency" NARROW []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000481 ! detector attribute
relationship: has_units UO:0000106 ! hertz

[Term]
id: MS:1000030
name: vendor
def: "OBSOLETE Name of instrument vendor" [PSI:MS]
comment: This term was made obsolete because it was replaced by instrument model (MS:1000031)
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: "OBSOLETE" [PSI:MS]
comment: This term was made obsolete because...just because.
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: "OBSOLETE Acquisition time in minutes." [PSI:MS]
comment: This term was made obsolete because it was replaced by scan time (MS:1000016)
is_obsolete: true

[Term]
id: MS:1000039
name: second
def: "OBSOLETE Acquisition time in seconds." [PSI:MS]
comment: This term was made obsolete because it was replaced by scan time (MS:1000016)
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:0000266 ! electronvolt

[Term]
id: MS:1000046
name: energy unit
def: "OBSOLETE Energy units are represented in either eV or Joules." [PSI:MS]
comment: This term was made obsolete because it was redundant with the Unit Ontology energy unit (UO:0000111)
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]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000548 ! sample attribute

[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: "OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. " [PSI:MS]
comment: This term was made obsolete because it was replaced by electron ionization (MS:1000389)
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: "OBSOLETE" [PSI:MS]
comment: This term was made obsolete because it was replaced by negative scan (MS:1000129)
is_obsolete: true

[Term]
id: MS:1000077
name: positive ion mode
def: "OBSOLETE" [PSI:MS]
comment: This term was made obsolete because it was replaced by positive scan (MS:1000130)
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: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS]
comment: This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206)
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:1000479 ! purgatory

[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:1000479 ! purgatory

[Term]
id: MS:1000102
name: single ion monitoring
def: "OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum." [PSI:MS]
comment: This term was made obsolete because it was replaced by single ion monitoring (MS:100205)
is_obsolete: true

[Term]
id: MS:1000103
name: single reaction monitoring
def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS]
comment: This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206)
is_obsolete: true

[Term]
id: MS:1000104
name: None  ??
def: "OBSOLETE None." [PSI:MS]
comment: This term was made obsolete because...just because.
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 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 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: "OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS]
comment: This term was made obsolete because it was redundant with the Unit Ontology electron volt (UO:0000266)
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: MS:1000510 ! precursor activation attribute

[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:1000479 ! purgatory

[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:1000479 ! purgatory

[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]
synonym: "AE" EXACT []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000266 ! electronvolt

[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]
synonym: "z" EXACT []
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute

[Term]
id: MS:1000212
name: dalton
def: "OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS]
comment: This term was made obsolete because it was redundant with the Unit Ontology dalton (UO:0000221)
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]
synonym: "EA" EXACT []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
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: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS]
comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392)
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]
synonym: "IE" EXACT []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute
relationship: has_units UO:0000266 ! electronvolt

[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: "OBSOLETE The height or area of a peak in a mass spectrum." [PSI:MS]
comment: This term was made obsolete because it was replaced by base peak intensity (MS:1000505)
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]
synonym: "PA" EXACT [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000507 ! ion attribute

[Term]
id: MS:1000234
name: mass resolving power
def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS]
comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800)
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000444 ! m/z Separation Method
is_obsolete: true

[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:1000810 ! mass chromatogram

[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: "OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg." [PSI:MS]
comment: This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221)
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: "OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS]
comment: This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382)
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:1000479 ! purgatory

[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: "OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS]
comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393)
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: "OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS]
comment: This term was made obsolete because it was replaced by surface ionization (MS:1000406)
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: "OBSOLETE Mass spectrometry using spark ionization." [PSI:MS]
comment: This term was made obsolete because it was replaced by spark ionization (MS:1000404)
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 []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute

[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:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[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:0000218 ! volt

[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]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000487 ! ion optics attribute
relationship: has_units UO:0000268 ! volt per meter

[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
is_a: MS:1000524 ! data file content

[Term]
id: MS:1000323
name: constant neutral loss scan
def: "Spectrum of all precursor ions that undergo a selected m/z decrement." [PSI:MS]
synonym: "constant neutral mass loss scan" RELATED []
synonym: "fixed neutral fragment scan" RELATED []
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000324
name: constant neutral gain scan
def: "Spectrum of all precursor ions that undergo a selected m/z increment." [PSI:MS]
synonym: "Constant Neutral Mass Gain Scan" EXACT []
is_a: MS:1000479 ! purgatory

[Term]
id: MS:1000325
name: constant neutral 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]
synonym: "constant neutral mass gain spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

[Term]
id: MS:1000326
name: constant neutral 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 spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

[Term]
id: MS:1000327
name: consecutive reaction monitoring
def: "OBSOLETE 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." [PSI:MS]
comment: This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244)
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 ?
is_a: MS:1001055 ! modification parameters

[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: "OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions." [PSI:MS]
comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580)
is_a: MS:1000343 ! product ion spectrum
is_obsolete: true

[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: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z" [PSI:MS]
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

[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: "OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS]
comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580)
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content
is_obsolete: true

[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: "OBSOLETE A product ion that results from the dissociation of a precursor ion." [PSI:MS]
comment: This term was made obsolete because it was replaced by product ion (MS:1000342)
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:1000479 ! purgatory

[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]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
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]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
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:1001458 ! spectrum generation information

[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:1001458 ! spectrum generation information

[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]
synonym: "analyzer" EXACT []
relationship: part_of MS:1000463 ! instrument

[Term]
id: MS:1000452
name: data transformation
def: "Terms used to describe types of data processing." [PSI:MS]
synonym: "data processing" EXACT []
relationship: part_of MS:1001458 ! spectrum generation information

[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]
synonym: "activation" EXACT []
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1000457
name: sample
def: "Terms to describe the sample." [PSI:MS]
relationship: part_of MS:1001458 ! spectrum generation information

[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:1001458 ! spectrum generation information

[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]
synonym: "instrument configuration" EXACT []
relationship: part_of MS:1001458 ! spectrum generation information

[Term]
id: MS:1000464
name: mass unit
def: "OBSOLETE A unit of measurement for mass." [PSI:MS]
comment: This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002)
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: "OBSOLETE Alternating." [PSI:MS]
comment: This term was made obsolete because...just because.
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:1001458 ! spectrum generation information

[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:0000218 ! volt

[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: "Special scan mode, where data with improved resoltuion is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS]
synonym: "enhanced resolution scan" EXACT []
is_a: MS:1000499 ! spectrum attribute

[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 window upper limit
def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS]
synonym: "mzRangeStop" RELATED []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000549 ! selection window attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000501
name: scan window lower limit
def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS]
synonym: "mzRangeStart" RELATED []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
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]
synonym: "Scan Duration" RELATED []
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[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 signal of highest intensity 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
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second

[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:0000266 ! electronvolt

[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:1000499 ! spectrum 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 m/z 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
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000814 ! counts per second

[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: "Encoding type of binary data, e.g. 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: "OBSOLETE Signed 32-bit integer." [PSI:MS]
is_a: MS:1000518 ! binary data type
is_obsolete: true

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

[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: "OBSOLETE Signed 64-bit integer." [PSI:MS]
is_a: MS:1000518 ! binary data type
is_obsolete: true

[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 ! raw 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: Waters raw file
def: "Waters data file found in a Waters RAW directory, generated from an MS acquisition." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1000527
name: highest observed m/z
def: "Highest m/z value observed in the m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
is_a: MS:1000808 ! chromatogram attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000528
name: lowest observed m/z
def: "Lowest m/z value observed in the m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
is_a: MS:1000808 ! chromatogram 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 Vocabularies

[Term]
id: MS:1000532
name: Xcalibur
def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS]
is_a: MS:1000693 ! Thermo Finnigan software
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000534
name: MassLynx
def: "Micromass software for data acquisition and analysis." [PSI:MS]
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000535
name: FlexAnalysis
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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]
synonym: "wolf" EXACT []
is_a: MS:1001457 ! data processing software

[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
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000540
name: FlexControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001455 ! acquisition 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:1001457 ! data processing 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:1001457 ! data processing 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:1001458 ! spectrum generation information

[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: "OBSOLETE Time Unit." [PSI:MS]
comment: This term was made obsolete because it was redundant with the Unit Ontology time unit (UO:0000003)
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
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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:1001457 ! data processing 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: mass spectrometer file format
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]
is_a: MS:1001459 ! file format

[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 ! raw data file

[Term]
id: MS:1000562
name: ABI WIFF file
def: "Applied Biosystems WIFF file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1000563
name: Thermo RAW file
def: "Thermo Scientific RAW file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

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

[Term]
id: MS:1000565
name: Micromass PKL file
def: "Micromass PKL file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

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

[Term]
id: MS:1000567
name: Bruker/Agilent YEP file
def: "Bruker/Agilent YEP file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[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]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000561 ! data file checksum type

[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]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000561 ! data file checksum type

[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: raw data file
def: "Describes the type of file and its content." [PSI:MS]
synonym: "source file" EXACT []
relationship: part_of MS:1001458 ! spectrum generation information

[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: "Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment." [PSI:MS]
synonym: "full spectrum" EXACT []
synonym: "Q1 spectrum" EXACT []
synonym: "Q3 spectrum" EXACT []
synonym: "Single-Stage Mass Spectrometry" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

[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 []
synonym: "nth generation product ion spectrum" EXACT []
synonym: "product ion spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

[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:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

[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]
synonym: "MIM spectrum" EXACT []
synonym: "multiple ion monitoring spectrum" EXACT []
synonym: "selected ion monitoring spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

[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]
synonym: "MRM spectrum" EXACT []
synonym: "multiple reaction monitoring spectrum" EXACT []
synonym: "selected reaction monitoring spectrum" EXACT []
is_a: MS:1000294 ! mass spectrum
is_a: MS:1000524 ! data file content

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

[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:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

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

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

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

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

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

[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:1001457 ! data processing 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:0000010 ! second
relationship: has_units UO:0000031 ! minute

[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:1001458 ! spectrum generation information

[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:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000601
name: ProteinLynx Global Server
def: "Waters software for data analysis." [PSI:MS]
is_a: MS:1000694 ! Waters software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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: "Sequest DTA file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[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 ! mass spectrometer file format

[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:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute

[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
relationship: has_units UO:0000018 ! nanometer

[Term]
id: MS:1000618
name: highest observed wavelength
def: "Highest wavelength observed in an EMR spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
is_a: MS:1000808 ! chromatogram attribute
relationship: has_units UO:0000018 ! nanometer

[Term]
id: MS:1000619
name: lowest observed wavelength
def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
is_a: MS:1000808 ! chromatogram attribute
relationship: has_units UO:0000018 ! nanometer

[Term]
id: MS:1000620
name: PDA spectrum
def: "OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS]
comment: This term was made obsolete because it was replaced by absorption spectrum (MS:1000806)
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type
is_obsolete: true

[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:1001458 ! spectrum generation information

[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:1000810 ! mass chromatogram

[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:1000810 ! mass chromatogram

[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
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second

[Term]
id: MS:1000630
name: data processing parameter
def: "Data processing parameter used in the data processing performed on the data file." [PSI:MS]
relationship: part_of MS:1001458 ! spectrum generation information

[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
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second

[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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software

[Term]
id: MS:1000679
name: MassHunter Easy Access
def: "Software for open access data acquisition." [PSI:MS]
is_a: MS:1000689 ! Agilent software
is_a: MS:1001455 ! acquisition 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000682
name: MassHunter Metabolite ID
def: "Software for identification of metabolites." [PSI:MS]
is_a: MS:1000689 ! Agilent software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000683
name: MassHunter BioConfirm
def: "Software for protein characterization." [PSI:MS]
is_a: MS:1000689 ! Agilent software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software

[Term]
id: MS:1000707
name: BioTools
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000708
name: CLINPROT
def: "Bruker CLINPROT software." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000709
name: CLINPROT micro
def: "Bruker CLINPROT micro software." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000714
name: Compass for micrOTOF
def: "Bruker Compass for micrOTOF software." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000715
name: Compass OpenAccess
def: "Bruker compass OpenAccess software." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000718
name: CompassXtract
def: "Bruker software library for data access." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000719
name: DataAnalysis
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000720
name: dpControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001455 ! acquisition software

[Term]
id: MS:1000721
name: esquireControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001455 ! acquisition software

[Term]
id: MS:1000722
name: flexImaging
def: "Bruker software for data analysis." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001455 ! acquisition software

[Term]
id: MS:1000726
name: micrOTOFcontrol
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001455 ! acquisition 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1000737
name: spControl
def: "Bruker software for data acquisition." [PSI:MS]
is_a: MS:1000692 ! Bruker software
is_a: MS:1001455 ! acquisition 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 ! mass spectrometer file format

[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 ! mass spectrometer file format
is_a: MS:1001040 ! intermediate analysis format

[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 ion m/z
def: "Mass-to-charge ratio of the ion selected for fragmentation" [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
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]
xref: value-type:xsd\:date "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

[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:1001456 ! analysis software
is_a: MS:1001457 ! data processing 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 ! raw data file

[Term]
id: MS:1000768
name: Thermo nativeID format
def: "controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger." [PSI:MS]
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: "binomial smoothing" EXACT []
synonym: "Weierstrass transform" 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

[Term]
id: MS:1000786
name: non-standard data array
def: "A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1000787
name: inclusive low intensity threshold
def: "Threshold at or 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
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second

[Term]
id: MS:1000788
name: inclusive high intensity threshold
def: "Threshold at or 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
relationship: has_units MS:1000131 ! number of counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second

[Term]
id: MS:1000789
name: enhanced multiply charged spectrum
def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions" [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000579 ! MS1 spectrum

[Term]
id: MS:1000790
name: time-delayed fragmentation spectrum
def: "MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation" [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000580 ! MSn spectrum

[Term]
id: MS:1000791
name: enhanced resolution scan
def: "OBSOLETE Scan with enhanced resolution." [PSI:MS]
comment: This term was made obsolete because it was merged with zoom scan (MS:1000497)
is_a: MS:1000020 ! scanning method
is_obsolete: true

[Term]
id: MS:1000792
name: isolation window attribute
def: "Isolation window parameter." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000441 ! scan

[Term]
id: MS:1000793
name: isolation window upper limit
def: "OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS]
comment: This term was obsoleted in favor of using a target, lower, upper offset scheme. See terms 1000827-1000829
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z
is_obsolete: true

[Term]
id: MS:1000794
name: isolation window lower limit
def: "OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS]
comment: This term was obsoleted in favor of using a target, lower, upper offset scheme. See terms 1000827-1000829
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z
is_obsolete: true

[Term]
id: MS:1000795
name: no combination
def: "Use this term if only one scan was recorded or there is no information about scans available." [PSI:MS]
is_a: MS:1000570 ! spectra combination

[Term]
id: MS:1000796
name: spectrum title
def: "A free-form text title describing a spectrum." [PSI:MS]
comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1000797
name: peak list scans
def: "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1000798
name: peak list raw scans
def: "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS]
comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000499 ! spectrum attribute
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1000799
name: custom unreleased software tool
def: "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000531 ! software

[Term]
id: MS:1000800
name: mass resolving power
def: "The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1000801
name: area peak picking
def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported." [PSI:MS]
synonym: "sum peak picking" EXACT []
is_a: MS:1000035 ! peak picking

[Term]
id: MS:1000802
name: height peak picking
def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported." [PSI:MS]
synonym: "max peak picking" EXACT []
is_a: MS:1000035 ! peak picking

[Term]
id: MS:1000803
name: analyzer scan offset
def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS]
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:1000804
name: electromagnetic radiation spectrum
def: "A plot of the relative intensity of electromagnetic radiation as a function of the wavelength." [PSI:MS]
synonym: "EMR spectrum" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000805
name: emission spectrum
def: "A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000806
name: absorption spectrum
def: "A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000559 ! spectrum type

[Term]
id: MS:1000807
name: Th/s
def: "Unit describing the scan rate of a spectrum in Thomson per second." [PSI:MS]
is_a: MS:1000460 ! unit

[Term]
id: MS:1000808
name: chromatogram attribute
def: "Chromatogram properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000625 ! chromatogram

[Term]
id: MS:1000809
name: chromatogram title
def: "A free-form text title describing a chromatogram." [PSI:MS]
comment: This is the preferred storage place for the spectrum title.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000808 ! chromatogram attribute

[Term]
id: MS:1000810
name: mass chromatogram
def: "A plot of the relative abundance of a beam or other collection of ions as a function of the retention time." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type

[Term]
id: MS:1000811
name: electromagnetic radiation chromatogram
def: "The measurement of electromagnetic properties as a function of the retention time." [PSI:MS]
synonym: "EMR radiation chromatogram" EXACT []
is_a: MS:1000524 ! data file content
is_a: MS:1000626 ! chromatogram type

[Term]
id: MS:1000812
name: absorption chromatogram
def: "The measurement of light absorbed by the sample as a function of the retention time." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000811 ! electromagnetic radiation chromatogram

[Term]
id: MS:1000813
name: emission chromatogram
def: "The measurement of light emitted by the sample as a function of the retention time." [PSI:MS]
is_a: MS:1000524 ! data file content
is_a: MS:1000811 ! electromagnetic radiation chromatogram

[Term]
id: MS:1000814
name: counts per second
def: "The number of counted events observed per second in one or a group of elements of a detector." [PSI:MS]
is_a: MS:1000043 ! intensity unit

[Term]
id: MS:1000815
name: Bruker BAF file
def: "Bruker BAF raw file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1000816
name: Bruker U2 file
def: "Bruker HyStar U2 file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1000817
name: HyStar
def: "Bruker software for hyphenated experiments." [PSI:MS]
is_a: MS:1000692 ! Bruker software

[Term]
id: MS:1000818
name: Acquity UPLC PDA
def: "Acquity UPLC Photodiode Array Detector." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000819
name: Acquity UPLC FLR
def: "Acquity UPLC Fluorescence Detector." [PSI:MS]
is_a: MS:1000126 ! Waters instrument model

[Term]
id: MS:1000820
name: flow rate array
def: "A data array of flow rate measurements." [PSI:MS]
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1000821
name: pressure array
def: "A data array of pressure measurements." [PSI:MS]
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000110 ! pascal

[Term]
id: MS:1000822
name: temperature array
def: "A data array of temperature measurements." [PSI:MS]
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000012 ! kelvin

[Term]
id: MS:1000823
name: Bruker U2 nativeID format
def: "declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000824
name: no nativeID format
def: "No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1000825
name: Bruker FID file
def: "Bruker FID file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1000826
name: elution time
def: "The time of elution from a chromatographic column, relative to the start of the chromatography." [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:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1000827
name: isolation window target m/z
def: "The primary or reference m/z about which the isolation window is defined." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000828
name: isolation window lower offset
def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymetric about the target m/z." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000829
name: isolation window upper offset
def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymetric about the target m/z." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000792 ! isolation window attribute
relationship: has_units MS:1000040 ! m/z

[Term]
id: MS:1000831
name: sample preparation
def: "Properties of the preparation steps which took place before the measurement was performed." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000548 ! sample

[Term]
id: MS:1000832
name: MALDI matrix application
def: "Attributes to describe the technique how the sample is prepared with the matrix solution." [PSI:MS]
relationship: part_of MS:1000831 ! Matrix-Assisted Laser Desorption Ionisation

[Term]
id: MS:1000833
name: matrix application type
def: "Describes the technique how the matrix is put on the sample target." [PSI:MS]
relationship: part_of MS:1000832 ! Matrix-Assisted Laser Desorption Ionisation Attributes

[Term]
id: MS:1000834
name: matrix solution
def: "Describes the chemical solution used as matrix." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: is_a MS:1000832 ! Matrix-Assisted Laser Desorption Ionisation Attributes

[Term]
id: MS:1000835
name: matrix solution concentration
def: "Concentration of the chemical solution used as matrix." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000832 ! Matrix-Assisted Laser Desorption Ionisation Attributes
relationship: has_units UO:0000051 ! Concentration Unit

[Term]
id: MS:1000836
name: dried dropplet
def: "Def." [PSI:MS]
relationship: is_a MS:1000833 ! Matrix Application Type

[Term]
id: MS:1000837
name: printed
def: "Def." [PSI:MS]
relationship: is_a MS:1000833 ! Matrix Application Type

[Term]
id: MS:1000838
name: sprayed
def: "Def." [PSI:MS]
relationship: is_a MS:1000833 ! Matrix Application Type

[Term]
id: MS:1000839
name: precoated plate
def: "Def." [PSI:MS]
relationship: is_a MS:1000833 ! Matrix Application Type

[Term]
id: MS:1000840
name: laser
def: "Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation." [PSI:MS]
relationship: part_of MS:1000482 ! source attribute

[Term]
id: MS:1000841
name: laser attribute
def: "Laser properties that are associated with a value." [PSI:MS]
relationship: part_of MS:1000840 ! Laser

[Term]
id: MS:1000842
name: laser type
def: "Type of laser used used fpr desorption purpose." [PSI:MS]
relationship: part_of MS:1000840 ! Laser

[Term]
id: MS:1000843
name: wavelength
def: "The distance between two peaks of the emitted laser beam." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000841 ! Laser Attribute
relationship: has_units UO:0000001 ! Lenght Unit

[Term]
id: MS:1000844
name: focus diameter x
def: "Describes the diameter of the laser beam in x direction." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000841 ! Laser Attribute
relationship: has_units UO:0000001 ! Lenght Unit

[Term]
id: MS:1000845
name: focus diameter y
def: "Describes the diameter of the laser beam in y direction." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000841 ! Laser Attribute
relationship: has_units UO:0000001 ! Lenght Unit

[Term]
id: MS:1000846
name: pulse energy
def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000841 ! Laser Attribute
relationship: has_units UO:0000111 ! Energy Unit

[Term]
id: MS:1000847
name: pulse duration
def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000841 ! Laser Attribute
relationship: has_units UO:0000003 ! Time Unit

[Term]
id: MS:1000848
name: attenuation
def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000841 ! Laser Attribute
relationship: has_units UO:0000003 ! Time Unit

[Term]
id: MS:1000849
name: impact angle
def: "Describes the angle between the laser beam and the sample target." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
relationship: is_a MS:1000841 ! Laser Attribute
relationship: has_units UO:0000121 ! Angle Unit

[Term]
id: MS:1000850
name: gas laser
def: "Laser which is powered by a gaseous medium." [PSI:MS]
relationship: is_a MS:1000842 ! Laser Type

[Term]
id: MS:1000851
name: solid-state laser
def: "Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states." [PSI:MS]
relationship: is_a MS:1000842 ! Laser Type

[Term]
id: MS:1000852
name: dye-laser
def: "Dye lasers use an organic dye as the gain medium." [PSI:MS]
relationship: is_a MS:1000842 ! Laser Type

[Term]
id: MS:1000853
name: free electron laser
def: "Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term." [PSI:MS]
relationship: is_a MS:1000842 ! Laser Type

[Term]
id: MS:1000854
name: LTQ XL
def: "Thermo Scientific LTQ XL MS." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000855
name: LTQ Velos
def: "Thermo Scientific LTQ Velos MS." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000856
name: LTQ Velos ETD
def: "Thermo Scientific LTQ Velos MS with ETD." [PSI:MS]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1000857
name: run attribute
def: "Properties of the described run." [PSI:MS]

[Term]
id: MS:1000858
name: fraction identifier
def: "Identier string that describes the sample fraction. This identifer should contain the fraction number(s) or similar information." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000857 ! run attribute

[Term]
id: MS:1000859
name: molecule
def: "A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction." [PSI:MS]
relationship: part_of MS:1000881 ! chemical compound

[Term]
id: MS:1000860
name: peptide
def: "A compound of low molecular weight that is composed of two or more amino acids." [PSI:MS]
is_a: MS:1000881 ! chemical compound

[Term]
id: MS:1000861
name: chemical compound attribute
def: "A describable property of a chemical compound." [PSI:MS]
relationship: part_of MS:1000881 ! chemical compound

[Term]
id: MS:1000862
name: isoelectric point
def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS]
exact_synonym: "pI" []
is_a: MS:1000861 ! chemical compound attribute

[Term]
id: MS:1000863
name: predicted isoelectric point
def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS]
exact_synonym: "predicted pI" []
is_a: MS:1000862 ! isoelectric point

[Term]
id: MS:1000864
name: chemical compound formula
def: "A combination of symbols used to express the chemical composition of a compound." [PSI:MS]
relationship: part_of MS:1000881 ! chemical compound

[Term]
id: MS:1000865
name: empirical formula
def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS]
is_a: MS:1000864 ! chemical compound formula

[Term]
id: MS:1000866
name: molecular formula
def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS]
is_a: MS:1000864 ! chemical compound formula

[Term]
id: MS:1000867
name: structural formula
def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS]
is_a: MS:1000864 ! chemical compound formula

[Term]
id: MS:1000868
name: SMILES string
def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [PSI:MS]
is_a: MS:1000864 ! chemical compound formula

[Term]
id: MS:1000869
name: collision gas pressure
def: "The gas pressure of the collision gas used for collisional excitation." [PSI:MS]
xref_analog: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000510 ! precursor activation attribute
relationship: has_units UO:0000110 ! pascal

[Term]
id: MS:1000870
name: 4000 QTRAP
def: "AB SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000." [PSI:MS]
is_a: MS:1000121 ! AB SCIEX instrument model

[Term]
id: MS:1000871
name: SRM software
def: "Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000872
name: MaRiMba
def: "SRM software used to select candidate SRM transitions from a spectral library." [PSI:MS]
is_a: MS:1000711 ! SRM software

[Term]
id: MS:1000873
name: peptide attribute calculation software
def: "Software used to predict or calculate numberical attributes of peptides." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1000874
name: SSRCalc
def: "Sequence Specific Retention Calculator esimates the retention time of peptides based on their sequence. It is available at http://hs2.proteome.ca/SSRCalc/SSRCalc.html." [PSI:MS]
is_a: MS:1000873 ! peptide attribute calculation software

[Term]
id: MS:1000875
name: declustering potential
def: "Potential difference between the orifice and the skimmer 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:0000218 ! volt

[Term]
id: MS:1000876
name: cone voltage
def: "Potential difference between the sampling cone/orifice and the what? 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:0000218 ! volt

[Term]
id: MS:1000877
name: tube lens
def: "No ideas." [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:0000218 ! volt

[Term]
id: MS:1000878
name: external reference identifier
def: "An identifier/accession number to an external reference database." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

[Term]
id: MS:1000879
name: PubMed identifier
def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference

[Term]
id: MS:1000880
name: interchannel delay
def: "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS]
xref_analog: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second

[Term]
id: MS:1000881
name: chemical compound
def: "A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

[Term]
id: MS:1001000
name: spectrum interpretation
def: "Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

[Term]
id: MS:1001005
name: sequest:CleavesAt
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001006
name: sequest:ViewCV
def: "Branch containing the CV terms for Sequest View Input Parameters." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001007
name: sequest:OutputLines
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001009
name: sequest:DescriptionLines
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001010
name: de novo search
def: "A de novo sequencing search (without database)." [PSI:PI]
is_a: MS:1001080 ! search type

[Term]
id: MS:1001011
name: search database details
def: "Details about the database searched." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001012
name: database source
def: "The organisation, project or laboratory from where the database is obtained (uniprot, ncbi, ebi, other)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001013
name: database name
def: "The name of the search database (nr, SwissProt or est_human)." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001014
name: database local file path
def: "Local file path of the search database from the search engine's point of view." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001015
name: database original uri
def: "URI, from where the search database was originally downloaded." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001016
name: database version
def: "Version of the search database ." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001017
name: database release date
def: "Release date of the search database." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001018
name: database type
def: "Database containing amino acid or nucleic acid sequences." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001019
name: database filtering
def: "Was there filtering used on the database(s), public or private." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001020
name: DB filter taxonomy
def: "The taxonomy filter applied (if any) to the database search." [PSI:PI]
is_a: MS:1001019 ! database filtering

[Term]
id: MS:1001021
name: DB filter on accession numbers
def: "Filtering applied specifically by accession number pattern." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001019 ! database filtering

[Term]
id: MS:1001022
name: DB MW filter
def: "Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001019 ! database filtering

[Term]
id: MS:1001023
name: DB PI filter
def: "Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001019 ! database filtering

[Term]
id: MS:1001024
name: translation frame
def: "The translated open reading frames from a nucleotide database considered in the search (range: 1-6)." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001025
name: translation table
def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001026
name: sequest:NormalizeXCorrValues
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001027
name: DB filter on sequences
def: "Filtering applied specifically by amino acid sequence pattern." [PSI:PI]
is_a: MS:1001019 ! database filtering

[Term]
id: MS:1001028
name: sequest:SequenceHeaderFilter
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001029
name: number of sequences searched
def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001030
name: number of peptide seqs compared to each spectrum
def: "Number of peptide seqs compared to each spectrum." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001031
name: spectral library search
def: "A search using a library of spectra." [PSI:PI]
is_a: MS:1001080 ! search type

[Term]
id: MS:1001032
name: sequest:SequencePartialFilter
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001035
name: date / time search performed
def: "Date and time of the actual search run." [PSI:PI]
is_a: MS:1001184 ! search statistics

[Term]
id: MS:1001036
name: search time taken
def: "The time taken to complete the search in seconds." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001184 ! search statistics

[Term]
id: MS:1001037
name: sequest:ShowFragmentIons
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001038
name: sequest:Consensus
def: "Specify depth as value of the CVParam!" [PSI:PI]
is_a: MS:1001006 ! sequest:ViewCV

[Term]
id: MS:1001040
name: intermediate analysis format
def: "Type of the source file, the  mzIdentML was created from." [PSI:PI]
is_a: MS:1001459 ! file format

[Term]
id: MS:1001041
name: sequest:sortCV
def: "Branch containing the CV terms for Sequest View / Sort Input Parameters." [PSI:PI]
is_a: MS:1001006 ! sequest:ViewCV

[Term]
id: MS:1001042
name: sequest:LimitTo
def: "Specify \"number of dtas shown\" as value of the CVParam!" [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001044
name: cleavage agent details
def: "Details of cleavage agent (enzyme)." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001045
name: cleavage agent name
def: "The name of the cleavage agent." [PSI:PI]
is_a: MS:1001044 ! cleavage agent details

[Term]
id: MS:1001046
name: sequest:sort_by_dCn
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001047
name: sequest:sort_by_dM
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001048
name: sequest:sort_by_Ions
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001049
name: sequest:sort_by_MH+
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001050
name: sequest:sort_by_P
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001051
name: multiple enzyme combination rules
def: "Description of multiple enzyme digestion protocol, if any." [PSI:PI]
is_a: MS:1001044 ! cleavage agent details

[Term]
id: MS:1001052
name: sequest:sort_by_PreviousAminoAcid
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001053
name: sequest:sort_by_Ref
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001055
name: modification parameters
def: "Modification parameters for the search engine run." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001056
name: modification specificity rule
def: "The specificity rules for the modifications applied by the search engine." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1001057
name: tolerance on types
def: "Tolerance on types." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1001058
name: quality estimation by manual validation
def: "The quality estimation was done manually." [PSI:PI]
is_a: MS:1001060 ! quality estimation details

[Term]
id: MS:1001059
name: sequest:sort_by_RSp
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001060
name: quality estimation details
def: "Method for quality estimation (manually or wih decoy database)." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001061
name: neutral loss
def: "OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD?" [PSI:PI]
is_a: MS:1001055 ! modification parameters
is_obsolete: true
replaced_by: MS:1000336 ! neutral loss

[Term]
id: MS:1001062
name: Mascot MGF file
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001065
name: TODOscoring model
def: "DELETE. There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms!" [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001066
name: ions series considered in search
def: "The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001068
name: sequest:sort_by_Sp
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001069
name: sequest:sort_by_TIC
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001070
name: sequest:sort_by_Scan
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001071
name: sequest:sort_by_Sequence
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001072
name: sequest:sort_by_Sf
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001073
name: database type AA
def: "Database contains amino acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

[Term]
id: MS:1001079
name: database type NA
def: "Database contains nucleid acid sequences." [PSI:PI]
is_a: MS:1001018 ! database type

[Term]
id: MS:1001080
name: search type
def: "Enumeration of type of search value (i.e. from PMF, sequence tag, MS-MS)." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001081
name: pmf search
def: "A peptide mass fingerprint search." [PSI:PI]
is_a: MS:1001080 ! search type

[Term]
id: MS:1001082
name: tag search
def: "A sequence tag search." [PSI:PI]
is_a: MS:1001080 ! search type

[Term]
id: MS:1001083
name: ms-ms search
def: "An ms/ms search (with fragment ions)." [PSI:PI]
is_a: MS:1001080 ! search type

[Term]
id: MS:1001084
name: database nr
is_a: MS:1001013 ! database name

[Term]
id: MS:1001085
name: protein result details
def: "Protein level information." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001086
name: sequest:sort_by_XCorr
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001087
name: sequest:ProcessCV
def: "Branch containing the CV terms for Sequest View / Process Input Parameters." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001088
name: protein description
def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001342 ! database sequence details

[Term]
id: MS:1001089
name: molecule taxonomy
def: "The taxonomy of the resultant molecule from the search." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001090
name: taxonomy nomenclature
def: "OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI]
is_a: MS:1001089 ! protein taxonomy
is_obsolete: true
replaced_by: MS:1001467 ! taxonomy: NCBI TaxID
replaced_by: MS:1001468 ! taxonomy: common name
replaced_by: MS:1001469 ! taxonomy: scientific name
replaced_by: MS:1001470 ! taxonomy: Swiss-Prot ID

[Term]
id: MS:1001091
name: NoEnzyme
is_a: MS:1001045 ! cleavage agent name

[Term]
id: MS:1001092
name: peptide quality estimation measure
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001093
name: coverage
def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI]
xref: value-type:xsd\:decimal "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

[Term]
id: MS:1001094
name: sequest:sort_by_z
xref: value-type:xsd\:bool "The allowed value-type for this CV term."
is_a: MS:1001041 ! sequest:sortCV

[Term]
id: MS:1001095
name: sequest:ProcessAll
is_a: MS:1001087 ! sequest:ProcessCV

[Term]
id: MS:1001096
name: sequest:TopPercentMostIntense
def: "Specify \"percentage\" as value of the CVParam!" [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001087 ! sequest:ProcessCV

[Term]
id: MS:1001097
name: distinct peptide sequences
def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

[Term]
id: MS:1001098
name: confident distinct peptide sequences
def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

[Term]
id: MS:1001099
name: confident peptide qualification
def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

[Term]
id: MS:1001100
name: confident peptide
def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details

[Term]
id: MS:1001101
name: protein group/subset relationship
def: "Branch containing protein group/subset relationships. TODO: add child terms." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001102
name: sequest:Chromatogram
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001006 ! sequest:ViewCV

[Term]
id: MS:1001103
name: sequest:InfoAndLog
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001006 ! sequest:ViewCV

[Term]
id: MS:1001104
name: database SwissProt
is_a: MS:1001013 ! database name

[Term]
id: MS:1001105
name: peptide result details
def: "Peptide level information." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001106
name: sequest:TopNumber
def: "Specify \"number\" as value of the CVParam!" [PSI:PI]
is_a: MS:1001087 ! sequest:ProcessCV

[Term]
id: MS:1001107
name: data stored in database
def: "Source file for this mzIdentML was a data set in a database." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001108
name: param: a ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001109
name: sequest:CullTo
def: "Specify cull string as value of the CVParam!" [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001087 ! sequest:ProcessCV

[Term]
id: MS:1001110
name: sequest:modeCV
def: "Branch containing the CV terms for Sequest Mode Input Parameters." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001111
name: sequest:Full
xref: value-type:xsd\:bool "The allowed value-type for this CV term."
is_a: MS:1001110 ! sequest:modeCV

[Term]
id: MS:1001112
name: n-terminal flanking residue
def: "The residue preceeding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001113
name: c-terminal flanking residue
def: "The residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001114
name: retention time(s)
def: "Retention time of the spectrum from the source file" [PSI:PI]
is_a: MS:1001105 ! peptide result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1001115
name: scan number(s)
def: "Take from mzData. TODO: What does this mean?" [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001116
name: single protein result details
def: "Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group)." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001117
name: theoretical mass
def: "The theoretical mass of the molecule (e.g. the peptide sequence and its modifications)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1001118
name: param: b ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001119
name: param: c ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001120
name: sequest:FormatAndLinks
xref: value-type:xsd\:bool "The allowed value-type for this CV term."
is_a: MS:1001110 ! sequest:modeCV

[Term]
id: MS:1001121
name: number of matched peaks
def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001122
name: ions series considered
def: "The ion series that were used during the calculation of the count (e.g. b, y, a, b, c, y, z, b, b-NH3, b-H20, b+, z, z-, z+, y-H3PO4, immonium)." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001123
name: number of peaks used
def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001124
name: number of peaks submitted
def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001125
name: manual validation
def: "Result of quality estimation: decision of a manual validation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide quality estimation measure
is_a: MS:1001198 ! protein quality estimation measure

[Term]
id: MS:1001126
name: sequest:Fast
xref: value-type:xsd\:bool "The allowed value-type for this CV term."
is_a: MS:1001110 ! sequest:modeCV

[Term]
id: MS:1001127
name: peptide sharing details
def: "Accessions Containing Sequence - Accessions for each protein containing this peptide." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001128
name: sequest:selectCV
def: "Branch containing the CV terms for Sequest Select Input Parameters." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001129
name: quantification information
def: "Quantification information." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001130
name: peptide raw areas
def: "Peptide raw areas." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001131
name: errors on peptide areas
def: "Errors on peptide areas." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001132
name: peptide ratios
def: "Peptide ratios." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001133
name: errors on peptide ratios
def: "Errors on peptide ratios." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001134
name: protein ratios
def: "Protein ratios." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001135
name: errors on protein ratios
def: "Errors on protein ratios." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001136
name: p-value (protein diff from 1 randomly)
def: "P-value (protein diff from 1 randomly)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001137
name: absolute quantities
def: "Absolute quantities." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001138
name: error on absolute quantity
def: "Error on absolute quantity." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001139
name: quantitation software name
def: "Quantitation software name." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001140
name: quantitation software version
def: "Quantitation software version." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001141
name: intensity of precursor ion
def: "The intensity of the precursor ion." [PSI:PI]
is_a: MS:1001129 ! quantification information

[Term]
id: MS:1001142
name: database IPI_human
is_a: MS:1001013 ! database name

[Term]
id: MS:1001143
name: search engine specific score for peptides
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001144
name: sequest:SelectDefault
is_a: MS:1001128 ! sequest:selectCV

[Term]
id: MS:1001145
name: TODOsequest:SelectAdvancedCV
def: "Branch containing the CV terms for Sequest Select Advanced Input Parameters." [PSI:PI]
is_a: MS:1001128 ! sequest:selectCV

[Term]
id: MS:1001146
name: param: a ion-NH3
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001147
name: protein ambiguity group result details
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001148
name: param: a ion-H2O
def: "Ion a - H2O if a significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001149
name: param: b ion-NH3
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001150
name: param: b ion-H2O
def: "Ion b - H2O if b significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001151
name: param: y ion-NH3
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001152
name: param: y ion-H2O
def: "Ion y - H2O if y significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001153
name: search engine specific score
def: "Search engine specific scores." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001154
name: sequest:probability
def: "The SEQUEST result 'Probability'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001155
name: sequest:xcorr
def: "The SEQUEST result 'Xcorr'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001156
name: sequest:deltacn
def: "The SEQUEST result 'DeltaCn'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001157
name: sequest:sp
def: "The SEQUEST result 'Sp' (protein)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001158
name: sequest:Uniq
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001159
name: sequest:expectation value
def: "The SEQUEST result 'Expectation value'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001160
name: sequest:sf
def: "The SEQUEST result 'Sf'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001161
name: sequest:matched ions
def: "The SEQUEST result 'Matched Ions'." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001162
name: sequest:total ions
def: "The SEQUEST result 'Total Ions'." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001163
name: sequest:consensus score
def: "The SEQUEST result 'Consensus Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001164
name: paragon:unused protscore
def: "The Paragon result 'Unused ProtScore'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001165
name: paragon:total protscore
def: "The Paragon result 'Total ProtScore'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001166
name: paragon:score
def: "The Paragon result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001167
name: paragon:confidence
def: "The Paragon result 'Confidence'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001168
name: paragon:expression error factor
def: "The Paragon result 'Expression Error Factor'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001169
name: paragon:expression change p-value
def: "The Paragon result 'Expression change P-value'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001170
name: paragon:contrib
def: "The Paragon result 'Contrib'." [PSI:PI]
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001171
name: mascot:score
def: "The Mascot result 'Score'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001172
name: mascot:expectation value
def: "The Mascot result 'expectation value'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001173
name: mascot:matched ions
def: "The Mascot result 'Matched ions'." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001174
name: mascot:total ions
def: "The Mascot result 'Total ions'." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001175
name: peptide shared in multiple proteins
is_a: MS:1001127 ! peptide sharing details

[Term]
id: MS:1001176
name: (?<=[KR])(?\!P)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001177
name: number of molecular hypothesis considered
def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI]
is_a: MS:1001184 ! search statistics

[Term]
id: MS:1001178
name: database EST
is_a: MS:1001013 ! database name

[Term]
id: MS:1001180
name: Cleavage agent regular expression
def: "Branch containing regular expressions for cleavage enzymes." [PSI:PI]
relationship: part_of MS:1001044 ! cleavage agent details

[Term]
id: MS:1001184
name: search statistics
def: "The details of the actual run of the search." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001189
name: modification specificity N-term
def: "As parameter for search engine: apply the modification only N-terminal." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:1001190
name: modification specificity C-term
def: "As parameter for search engine: apply the modification only C-terminal." [PSI:PI]
is_a: MS:1001056 ! modification specificity rule

[Term]
id: MS:1001191
name: p-value
def: "Quality estimation by p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide quality estimation measure
is_a: MS:1001198 ! protein quality estimation measure

[Term]
id: MS:1001192
name: Expect value
def: "Result of quality estimation: Expect value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide quality estimation measure
is_a: MS:1001198 ! protein quality estimation measure

[Term]
id: MS:1001193
name: confidence score
def: "Result of quality estimation: confidence score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide quality estimation measure
is_a: MS:1001198 ! protein quality estimation measure

[Term]
id: MS:1001194
name: quality estimation with decoy database
def: "Quality estimation by decoy database." [PSI:PI]
is_a: MS:1001060 ! quality estimation details

[Term]
id: MS:1001195
name: decoy DB type reverse
def: "Decoy type: Amino acids of protein sequences are used in reverse order." [PSI:PI]
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001196
name: decoy DB type randomized
def: "Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass)." [PSI:PI]
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001197
name: DB composition forward+decoy
def: "Decoy database composition: database contains original (forward) and decoy entries." [PSI:PI]
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001198
name: protein quality estimation measure
def: "Quality estimation score for a protein (p-value, Expect value, confidence, local FDR)." [PSI:PI]
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001199
name: Mascot DAT file
def: "Source file for this mzIdentML was a Mascot DAT file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001200
name: Sequest out file
def: "Source file for this mzIdentML was ONE Sequest out file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001201
name: DB MW filter maximum
is_a: MS:1001022 ! DB MW filter

[Term]
id: MS:1001202
name: DB MW filter minimum
is_a: MS:1001022 ! DB MW filter

[Term]
id: MS:1001203
name: DB PI filter maximum
is_a: MS:1001023 ! DB PI filter

[Term]
id: MS:1001204
name: DB PI filter minimum
is_a: MS:1001023 ! DB PI filter

[Term]
id: MS:1001207
name: Mascot
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001208
name: Sequest
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001209
name: Phenyx
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001210
name: mass type settings
def: "The type of mass difference value to be considered by the search engine (monoisotopic or average)." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001211
name: parent mass type mono
def: "Mass type setting for parent mass was monoisotopic." [PSI:PI]
is_a: MS:1001210 ! mass type settings

[Term]
id: MS:1001212
name: parent mass type average
def: "Mass type setting for parent mass was average isotopic." [PSI:PI]
is_a: MS:1001210 ! mass type settings

[Term]
id: MS:1001213 	 
name: search result details 	 
def: "OBSOLETE: Scores and global result characteristics." [PSI:PI]
relationship: part_of MS:1000479 ! purgatory
is_obsolete: true

[Term]
id: MS:1001214
name: prot:global FDR
def: "Estimation of global false discovery rate of the proteins." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001215
name: sequest:PeptideSp
def: "The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001217
name: sequest:PeptideRankSp
def: "The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001218
name: sequest:PeptideNumber
def: "The SEQUEST result '#' in out file (peptide)." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001219
name: sequest:PeptideIdnumber
def: "The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001220
name: frag: y ion
def: "Type of fragment: y ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001221
name: fragmentation information
def: "Fragmentation information like ion types." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001222
name: frag: b ion - H2O
def: "Type of fragment: b ion without water (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001223
name: frag: y ion - H2O
def: "Type of fragment: y ion without water (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001224
name: frag: b ion
def: "Type of fragment: b ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001225
name: product ion m/z
def: "The m/z of the product ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of the product ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001227
name: product ion m/z error
def: "The product ion m/z error (ADD more docu here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001228
name: frag: x ion
def: "Type of fragment: x ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001229
name: frag: a ion
def: "Type of fragment: a ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001230
name: frag: z ion
def: "Type of fragment: z ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001231
name: frag: c ion
def: "Type of fragment: c ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001232
name: frag: b ion - NH3
def: "Type of fragment: b ion without ammonium ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001233
name: frag: y ion - NH3
def: "Type of fragment: y ion without ammonium ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001234
name: frag: a ion - H2O
def: "Type of fragment: a ion without water (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001235
name: frag: a ion - NH3
def: "Type of fragment: a ion without ammonium ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001236
name: frag: d ion
def: "Type of fragment: d ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001237
name: frag: v ion
def: "Type of fragment: v ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001238
name: frag: w ion
def: "Type of fragment: w ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001239
name: frag: immonium ion
def: "Type of fragment: immonium ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001240
name: non-identified ion
def: "Non-identified ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001241
name: co-eluting ion
def: "Co-eluting ion (ADD more documentation here)." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001242
name: Sequest out folder
def: "Source file for this mzIdentML was a Sequest folder with its out files." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001243
name: Sequest summary
def: "Source file for this mzIdentML was a Sequest summary page (proteins)." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001245
name: PerSeptive PKS file
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001246
name: Sciex API III file
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001247
name: Bruker XML file
def: "Bruker data exchange xml." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001249
name: search input details
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001250
name: local FDR
def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001092 ! peptide quality estimation measure
is_a: MS:1001198 ! protein quality estimation measure
relationship: has_units UO:0000166 ! parts per notation
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1001251
name: Trypsin
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P)

[Term]
id: MS:1001252
name: DB source EBI
is_a: MS:1001012 ! database source

[Term]
id: MS:1001253
name: DB source NCBI
is_a: MS:1001012 ! database source

[Term]
id: MS:1001254
name: DB source UniProt
is_a: MS:1001012 ! database source

[Term]
id: MS:1001255
name: fragment mass type average
def: "Mass type setting for fragment mass was average isotopic." [PSI:PI]
is_a: MS:1001210 ! mass type settings

[Term]
id: MS:1001256
name: fragment mass type mono
def: "Mass type setting for fragment mass was monoisotopic." [PSI:PI]
is_a: MS:1001210 ! mass type settings

[Term]
id: MS:1001257
name: param: v ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001258
name: param: d ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001259
name: param: immonium ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001260
name: param: w ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001261
name: param: x ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001262
name: param: y ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001263
name: param: z ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001266
name: role type
def: "Role of a Person or Organization." [PSI:PI]
is_a: MS:1000585 ! contact person attribute

[Term]
id: MS:1001267
name: software vendor
is_a: MS:1001266 ! role type

[Term]
id: MS:1001268
name: programmer
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001269
name: instrument vendor
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001270
name: lab personnell
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001271
name: researcher
is_a: MS:1001266 ! role type

[Term]
id: MS:1001272
name: (?<=R)(?\!P)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001273
name: (?=[BD])
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001274
name: (?=[DE])
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001275
name: ProteinScape SearchEvent
def: "Source data for this mzIdentML was a ProteinScape SearchEvent." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001276
name: ProteinScape Gel
def: "Source data for this mzIdentML was a ProteinScape Gel." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001283
name: decoy DB accession regexp
def: "Specify the regular expression for decoy accession numbers." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001284
name: decoy DB derived from
def: "The name of the database, the search database was derived from." [PSI:PI]
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001285
name: database IPI_mouse
is_a: MS:1001013 ! database name

[Term]
id: MS:1001286
name: database IPI_rat
is_a: MS:1001013 ! database name

[Term]
id: MS:1001287
name: database IPI_zebrafish
is_a: MS:1001013 ! database name

[Term]
id: MS:1001288
name: database IPI_chicken
is_a: MS:1001013 ! database name

[Term]
id: MS:1001289
name: database IPI_cow
is_a: MS:1001013 ! database name

[Term]
id: MS:1001290
name: database IPI_arabidopsis
is_a: MS:1001013 ! database name

[Term]
id: MS:1001291
name: decoy DB from nr
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001292
name: decoy DB from IPI_rat
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001293
name: decoy DB from IPI_mouse
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001294
name: decoy DB from IPI_arabidopsis
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001295
name: decoy DB from EST
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001296
name: decoy DB from IPI_zebrafish
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001297
name: decoy DB from SwissProt
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001298
name: decoy DB from IPI_chicken
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001299
name: decoy DB from IPI_cow
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001300
name: decoy DB from IPI_human
is_a: MS:1001284 ! decoy DB derived from

[Term]
id: MS:1001301
name: protein rank
def: "The rank of the protein in a list sorted by the search engine." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1001302
name: search engine specific input parameter
def: "This branch contains search engine specific input parameters (e.g. Mascot Sig Threshold)." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001303
name: Arg-C
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001272 ! (?<=R)(?!P)

[Term]
id: MS:1001304
name: Asp-N
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001273 ! (?=[BD])

[Term]
id: MS:1001305
name: Asp-N_ambic
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001274 ! (?=[DE])

[Term]
id: MS:1001306
name: Chymotrypsin
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P)

[Term]
id: MS:1001307
name: CNBr
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001333 ! (?<=M)

[Term]
id: MS:1001308
name: Formic_acid
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D))

[Term]
id: MS:1001309
name: Lys-C
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001335 ! (?<=K)(?!P)

[Term]
id: MS:1001310
name: Lys-C/P
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001336 ! (?<=K)

[Term]
id: MS:1001311
name: PepsinA
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001337 ! (?<=[FL])

[Term]
id: MS:1001312
name: TrypChymo
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001338 ! (?<=[FYWLKR])(?!P)

[Term]
id: MS:1001313
name: Trypsin/P
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001339 ! (?<=[KR])

[Term]
id: MS:1001314
name: V8-DE
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001340 ! (?<=[BDEZ])(?!P)

[Term]
id: MS:1001315
name: V8-E
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001341 ! (?<=[EZ])(?!P)

[Term]
id: MS:1001316
name: mascot:SigThreshold
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001317
name: mascot:MaxProteinHits
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001318
name: mascot:ProteinScoringMethod
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001319
name: mascot:MinMSMSThreshold
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001320
name: mascot:ShowHomologousProteinsWithSamePeptides
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001321
name: mascot:ShowHomologousProteinsWithSubsetOfPeptides
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001322
name: mascot:RequireBoldRed
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001323
name: mascot:UseUnigeneClustering
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001324
name: mascot:IncludeErrorTolerantMatches
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001325
name: mascot:ShowDecoyMatches
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001326
name: TODO_add_others
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001328
name: OMSSA:evalue
def: "OMSSA E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001329
name: OMSSA:pvalue
def: "OMSSA p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001330
name: xtandem:expect
def: "The X!Tandem expectation value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001331
name: xtandem:hyperscore
def: "The X!Tandem hyperscore." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001332
name: (?<=[FYWL])(?\!P)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001333
name: (?<=M)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001334
name: ((?<=D))|((?=D))
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001335
name: (?<=K)(?\!P)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001336
name: (?<=K)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001337
name: (?<=[FL])
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001338
name: (?<=[FYWLKR])(?\!P)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001339
name: (?<=[KR])
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001340
name: (?<=[BDEZ])(?\!P)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001341
name: (?<=[EZ])(?\!P)
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1001342
name: database sequence details
def: "Details about a single database sequence." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001343
name: NA sequence
def: "The sequence is a nucleic acid sequence." [PSI:PI]
is_a: MS:1001342 ! database sequence details

[Term]
id: MS:1001344
name: AA sequence
def: "The sequence is a amino acid sequence." [PSI:PI]
is_a: MS:1001342 ! database sequence details

[Term]
id: MS:1001345
name: mass table source
def: "Children of this term specify the source of the mass table used." [PSI:PI]
is_a: MS:1001354 ! mass table options

[Term]
id: MS:1001346
name: AAIndex mass table
def: "The masses used in the mass table are taken from AAIndex." [PSI:PI]
is_a: MS:1001345 ! mass table source

[Term]
id: MS:1001347
name: database file formats
def: "The children of this term define file formats of the sequence database used." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001348
name: FASTA format
def: "The sequence database was stored in the FASTA format." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1001349
name: ASN.1
def: "The sequence database was storen in the ASN.1 format." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1001350
name: NCBI *.p*
def: "The sequence database was stored in the NCBI formatdb (*.p*) format." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1001351
name: clustal aln
def: "ClustalW ALN (multiple alignment) format." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1001352
name: embl em
def: "EMBL entry format." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1001353
name: NBRF PIR
def: "The NBRF PIR was used as format." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1001354
name: mass table options
def: "Root node for options for the mass table used." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001355
name: peptide descriptions
def: "Descriptions of peptides. TODO: What does this mean?" [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001356
name: spectrum descriptions
def: "Descriptions of the input spectra. TODO: really needed?" [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001357
name: spectrum quality descriptions
def: "Description of the quality of the input spectrum." [PSI:PI]
is_a: MS:1001356 ! spectrum descriptions

[Term]
id: MS:1001358
name: msmsEval quality
def: "This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001357 ! spectrum quality descriptions

[Term]
id: MS:1001359
name: ambiguous residues
def: "Children of this term describe abiguous residues." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001360
name: alternate single letter codes
def: "List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001359 ! ambiguous residues

[Term]
id: MS:1001361
name: alternate mass
def: "List of masses a non-standard letter code is replaced with." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001359 ! ambiguous residues

[Term]
id: MS:1001362
name: number of unmatched peaks
def: "The number of unmatched peaks." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001363
name: peptide unique to one protein
is_a: MS:1001127 ! peptide sharing details

[Term]
id: MS:1001364
name: pep:global FDR
def: "Estimation of global false discovery rate of the peptides." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001365
name: frag: internal yb ion
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001366
name: frag: internal ya ion
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001367
name: frag: z+1 ion
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001368
name: frag: z+2 ion
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001369
name: text file
def: "Simple text file of \"m/z [intensity]\" values for a PMF (or single MS-MS) search." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001370
name: mascot:homology threshold
def: "The Mascot result 'homology threshold'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001371
name: mascot:identity threshold
def: "The Mascot result 'identity threshold'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1001372
name: sequest:Sequences
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001373
name: sequest:TIC
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001374
name: sequest:Sum
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001375
name: Phenyx:Instrument Type
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001376
name: Phenyx:Scoring Model
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001377
name: Phenyx:Default Parent Charge
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001378
name: Phenyx:Trust Parent Charge
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001379
name: Phenyx:Turbo
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001380
name: Phenyx:Turbo:ErrorTol
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001381
name: Phenyx:Turbo:Coverage
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001382
name: Phenyx:Turbo:Series
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001383
name: Phenyx:MinPepLength
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001384
name: Phenyx:MinPepzscore
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001385
name: Phenyx:MaxPepPvalue
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001386
name: Phenyx:AC Score
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001387
name: Phenyx:Conflict Resolution
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001388
name: Phenyx:AC
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001389
name: Phenyx:ID
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001390
name: Phenyx:Score
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001391
name: Phenyx:Peptides1
def: "First number of phenyx result \"#Peptides\"." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001392
name: Phenyx:Peptides2
def: "Second number of phenyx result \"#Peptides\"." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001393
name: Phenyx:Auto
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001394
name: Phenyx:User
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001395
name: Phenyx:Pepzscore
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001396
name: Phenyx:PepPvalue
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001397
name: Phenyx:NumberOfMC
xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001398
name: Phenyx:Modif
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001399
name: OMSSA csv file
def: "Source file for this mzIdentML was an OMSSA csv file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001400
name: OMSSA xml file
def: "Source file for this mzIdentML was an OMSSA xml file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001401
name: xtandem xml file
def: "Source file for this mzIdentML was an X!Tandem xml file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001405
name: spectrum identification result details
def: "This subsection describes terms which can describe details of spectrum identification results." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001406
name: param: internal yb ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001407
name: param: internal ya ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001408
name: param: z+1 ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001409
name: param: z+2 ion
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001410
name: translation start codons
def: "The translation start codons used to translate the nucleotides to amino acids." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001411
name: search tolerance specification
is_a: MS:1001249 ! search input details

[Term]
id: MS:1001412
name: search tolerance plus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1001413
name: search tolerance minus value
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001411 ! search tolerance specification
relationship: has_units UO:0000166 ! parts per notation
relationship: has_units UO:0000187 ! percent
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1001414
name: MGF scans
def: "OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_obsolete: true
replaced_by: MS:1000797 ! peak list scans

[Term]
id: MS:1001415
name: MGF raw scans
def: "OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_obsolete: true
replaced_by: MS:1000798 ! peak list raw scans

[Term]
id: MS:1001416
name: spectrum title
def: "OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001405 ! spectrum identification result details
is_obsolete: true
replaced_by: MS:1000796 ! spectrum title

[Term]
id: MS:1001417
name: SpectraST:dot
def: "SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001418
name: SpectraST:dot_bias
def: "SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001419
name: SpectraST:discriminant score F
def: "SpectraST spectrum score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001420
name: SpectraST:delta
def: "SpectraST normalised difference between dot product of top hit and runner-up." [:PSI-PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001421
name: pepXML file
def: "Source file for this mzIdentML was a pepXML file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001422
name: protXML file
def: "Source file for this mzIdentML was a protXML file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001423
name: translation table description
def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001424
name: ProteinExtractor:Methodname
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001425
name: ProteinExtractor:GenerateNonRedundant
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001426
name: ProteinExtractor:IncludeIdentified
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001427
name: ProteinExtractor:MaxNumberOfProteins
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001428
name: ProteinExtractor:MaxProteinMass
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001429
name: ProteinExtractor:MinNumberOfPeptides
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001430
name: ProteinExtractor:UseMascot
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001431
name: ProteinExtractor:MascotPeptideScoreThreshold
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001432
name: ProteinExtractor:MascotUniqueScore
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001433
name: ProteinExtractor:MascotUseIdentityScore
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001434
name: ProteinExtractor:MascotWeighting
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001435
name: ProteinExtractor:UseSequest
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001436
name: ProteinExtractor:SequestPeptideScoreThreshold
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001437
name: ProteinExtractor:SequestUniqueScore
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001438
name: ProteinExtractor:SequestWeighting
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001439
name: ProteinExtractor:UseProteinSolver
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001440
name: ProteinExtractor:ProteinSolverPeptideScoreThreshold
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001441
name: ProteinExtractor:ProteinSolverUniqueScore
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001442
name: ProteinExtractor:ProteinSolverWeighting
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001443
name: ProteinExtractor:UsePhenyx
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001444
name: ProteinExtractor:PhenyxPeptideScoreThreshold
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001445
name: ProteinExtractor:PhenyxUniqueScore
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001446
name: ProteinExtractor:PhenyxWeighting
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001447
name: prot:FDR threshold
def: "False-discovery rate threshold for proteins." [PSI:PI]
is_a: MS:1001060 ! quality estimation details

[Term]
id: MS:1001448
name: pep:FDR threshold
def: "False-discovery rate threshold for peptides." [PSI:PI]
is_a: MS:1001060 ! quality estimation details

[Term]
id: MS:1001449
name: OMSSA e-value threshold
def: "Threshold for OMSSA e-value for quality estimation." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1001450
name: decoy DB details
def: "Details of decoy generation and database structure." [PSI:PI]
is_a: MS:1001011 ! search database details

[Term]
id: MS:1001451
name: decoy DB generation algorithm
def: "Name of algorithm used for decoy generation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001452
name: decoy DB type shuffle
def: "Decoy type: Amino acids of protein sequences are used in a random order." [PSI:PI]
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001453
name: DB composition only decoy
def: "Decoy database composition: database contains only decoy entries." [PSI:PI]
is_a: MS:1001450 ! decoy DB details

[Term]
id: MS:1001454
name: quality estimation with implicite decoy sequences
def: "Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy)." [PSI:PI]
is_a: MS:1001060 ! quality estimation details

[Term]
id: MS:1001455
name: acquisition software
def: "Acquisition software." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1001456
name: analysis software
def: "Analysis software." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1001457
name: data processing software
def: "Conversion software." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1001458
name: spectrum generation information
def: "Vocabularies describing the spectrum generation information." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

[Term]
id: MS:1001459
name: file format
def: "Format of data files." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

[Term]
id: MS:1001460
name: unknown modification
def: "This term should be given if the modification was unknown." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001471 ! peptide modification details

[Term]
id: MS:1001461
name: greylag
def: "greylag identification software, wee greylag.org." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001462
name: PEFF format
def: "The sequence database was stored in the PEFF (PSI enhanced FastA file) format." [PSI:PI]
is_a: MS:1001347 ! database file formats

[Term]
id: MS:1001463
name: Phenyx XML format
is_a: MS:1000560 ! mass spectrometer file format
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001464
name: DTASelect file
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001466
name: MS2 file
def: "MS2 file." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001467
name: taxonomy: NCBI TaxID
def: "This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001089 ! protein taxonomy

[Term]
id: MS:1001468
name: taxonomy: common name
def: "This term is used if a common name is specified, e.g. human." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001089 ! protein taxonomy


[Term]
id: MS:1001469
name: taxonomy: scientific name
def: "This term is used if a scientific name is specified, e.g. Homo sapiens." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001089 ! protein taxonomy


[Term]
id: MS:1001470
name: taxonomy: Swiss-Prot ID
def: "This term is used if a swiss prot taxonomy id is specified, e.g. Human." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001089 ! protein taxonomy

[Term]
id: MS:1001471
name: peptide modification details
def: "The children of this term can be used to describe modifications." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Typedef]
id: has_regexp
name: has regexp

[Typedef]
id: has_units
name: has_units

[Typedef]
id: part_of
name: part_of
is_transitive: true
python-pymzml 0.7.6-dfsg-4 / usr / lib / python2.7 / dist-packages / pymzml / obo / psi-ms-2.6.0.obo
