AFO Mass Spectrometry Domain Ontology (REC/2025/12)
type: Ontology
imports: afo
imports: detection
contributor: Allotrope Foundation
issued: 2025-12-16T12:00:00Z
license: Creative Commons Attribution 4.0 International Public License
license: iupac-license
modified: 2025-06-25T12:00:00Z
publisher: Allotrope Foundation
rights: Derivative works attribution
rights: Copyright © 2015-2025 Allotrope Foundation
rights holder: Allotrope Foundation
prior version: mass-spectrometry
version info: REC/2025/12

skimmer
type: Class
subclass of: ion optics
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
definition: A skimmer is a cone with a central orifice that intercepts the center of a spray or jet expansion to sample the central portion of the expansion, for example, as in a momentum separator. [IUPAC]

electron ionization source
type: Class
subclass of: AFE_0000004
alternative label: EI source
alternative label: electron impact source
definition: An electron ionization source is an ion source that consists of an ionization chamber and a thin strip of metal that is heated electrically to incandescence or a temperature at which it emits free electrons that are accelerated through a potential to an energy where they ionize the sample. [CHMO]

chemical ionization source
type: Class
subclass of: AFE_0000004
alternative label: CI source
definition: A chemical ionization source is an ion source that consists of a high-pressure ionization chamber containing a reagent gas (for example N2, O2 or H2O) which is ionized by high-energy electrons from a heated strip of metal and goes on to react with the analyte to ionize it. [CHMO]

quadrupole mass spectrometer
type: Class
subclass of: AFE_0000648
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: QMS
alternative label: quad-MS
definition: A piece of apparatus that consists of an ion source, a mass-to-charge analyzer, a detector and a vacuum system and is used to measure mass spectra. The detector is a quadrupole mass-to-charge analyzer, which holds the ions in a stable orbit by an electric field generated by four parallel electrodes. [IUPAC]

Paul ion trap
type: Class
subclass of: ion trap
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: QIT
alternative label: QUISTOR
alternative label: quadrupole ion storage trap
alternative label: quadrupole ion trap
definition: Ion trapping device that depends on the application of radio frequency potentials between a ring electrode and two end-cap electrodes to confine the ion motion to a cyclic path described by an appropriate form of the Mathieu equation. The choice of these potentials determines the m/z value below which ions are not trapped. [IUPAC]

ion trap
type: Class
subclass of: AFE_0000038
license: iupac-license
rights: iupac-copyright
source: A. G. Marshall, C. L. Hendrickson, G. S. Jackson. Mass Spectrom. Rev. 17, 1 (1998).
source: J. P. Holder, L. Gruber, H. E. DeWitt, B. R. Beck, D. A. Church, D. Schneider. Phys. Scr., T 92, 158 (2001).
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: IT
alternative label: LCQ
alternative label: LTQ
definition: A ion trap is a device for spatially confining ions using electric and magnetic fields alone or in combination. [IUPAC]

electrospray inlet
type: Class
subclass of: ion source inlet
alternative label: electrospray emitter
alternative label: electrospray needle
definition: Inlet used for introducing the liquid sample into an electrospray ionization source. [PSI/MS]

ion optics
type: Class
subclass of: AFE_0000354
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: ion guide
definition: Devices designed to control the formation, focusing, and deflection of charged particle beams in a vacuum under the influence of electric and magnetic fields. [IUPAC]

ion source inlet
type: Class
subclass of: AFE_0000462
definition: An ion source inlet is an inlet into an ion source of a mass spectrometer. [Allotrope]

single quadrupole mass spectrometer
type: Class
subclass of: quadrupole mass spectrometer
alternative label: SQD
alternative label: single quadrupole
definition: A single quadrupole mass spectrometer is a type of quadrupole mass spectrometer that uses one single quadrupole field. [Allotrope]

quadrupole
type: Class
subclass of: AFE_0000038
alternative label: quadripole
definition: A quadrupole is a mass-to-charge analyzer that holds the ions in a stable orbit by an electric field generated by four parallel electrodes. [Allotrope]

mass spectrometry system
type: Class
subclass of: AFE_0002141
alternative label: MS system
definition: A mass spectrometry system is a measuring system that is designed and assembled to realize the measurement function by way of mass spectrometry. [Allotrope]

mass spectrometer ionization source
type: Class
subclass of: AFE_0000004
subclass of: Restriction
  on property: BFO_0000050
  some values from: AFE_0000648
AFX_0002809: CHMO_0000960
alternative label: MS ionization source
alternative label: mass spectrometry ionization source
definition: A mass spectrometer ionization source is a piece of apparatus that takes an analyte and generates ions which are passed to the rest of a mass spectrometer for analysis. [CHMO]

filament (ms)
type: Class
subclass of: AFE_0000354
alternative label: filament
definition: A filament is a device that produces an electron stream to charge neutrals for analysis by mass spectrometry. [Allotrope]

collision energy (material entity)
type: Class
subclass of: AFM_0000880
alternative label: collision energy
definition: Collision energy is energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. [PSI/MS]

chemical ionization
type: Class
subclass of: AFP_0001993
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: CI
definition: Formation of a new ion in the gas phase by the reaction of a neutral with an ion. The process may involve transfer of an electron, a proton, or other charged species between the reactants. [IUPAC]
scope note: This term is not synonymous with chemi-ionization. [IUPAC]
scope note: 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. [IUPAC]

quadrupole mass spectrometry
type: Class
subclass of: AFP_0001427
alternative label: QMS
alternative label: quadrapole mass spectrometry
alternative label: quadrupolar mass spectrometry
alternative label: quadrupolar mass spectroscopy
alternative label: quadrupole mass spectroscopy
definition: Quadrapole mass spectrometry is a type of mass spectrometry where the mass-to-charge ratio of the sample ions is measured using an electric field generated by four parallel electrodes. [Allotrope]

electron ionization
type: Class
subclass of: AFP_0001993
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: EI
alternative label: electron impact
alternative label: electron impact ionization
definition: Electron ionization is a ionization that removes one or more electrons from an atom or molecule through interactions with electrons that are typically accelerated to energies between 10 and 150 eV. [IUPAC]

multiple-stage mass spectrometry
type: Class
subclass of: AFP_0001427
license: iupac-license
rights: iupac-copyright
source: G. L. Glish. Analyst 119, 533 (1994).
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: MSn
alternative label: MSn spectrometry
alternative label: MSn spectroscopy
alternative label: multiple-stage mass spectroscopy
definition: Multiple-stage mass spectrometry is a mass spectrometry where multiple stages of precursor ion m/z selection are followed by product ion detection for successive nth-generation product ions. [IUPAC]

selected reaction monitoring
type: Class
subclass of: multiple-stage mass spectrometry
license: iupac-license
rights: iupac-copyright
source: E. de Hoffmann (1996). Tandem Mass Spectrometry: a Primer. Journal of Mass Spectrometry 31: 129–137.
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: SRM
definition: Selected reaction monitoring is a multiple-stage mass spectrometry where data acquired from one or more specific product ions corresponding to m/z selected precursor ions are recorded via two or more stages of mass spectrometry. [IUPAC]
note: Selected reaction monitoring applied to multiple product ions from one or more precursor ions is known as multiple reaction monitoring. [IUPAC]
note: Selected reaction monitoring in multiple-stage mass spectrometry is known as consecutive reaction monitoring. [IUPAC]

electrospray ionization
type: Class
subclass of: spray ionization
license: iupac-license
rights: iupac-copyright
source: J. B. Fenn, M. Mann, C. K. Meng, S. F. Wong, C. M. Whitehouse. Science 246, 64 (1989).
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
source: M. Dole, L. L. Mack, R. L. Hines, R. C. Mobley, L. D. Ferguson, M. B. Alice. J. Chem. Phys. 49, 2240 (1968).
alternative label: ESI
alternative label: ionspray
definition: Spray ionization process in which either cations or anions in solution are transferred to the gas phase via formation and desolvation at atmospheric pressure of a stream of highly charged droplets that result from applying a potential difference between the tip of the electrospray needle containing the solution and a counter electrode. [IUPAC]
note: The term ionspray is deprecated unless describing the commercial product.

selected ion monitoring
type: Class
subclass of: AFP_0001427
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: SIM
alternative label: SIR
alternative label: selected ion recording
definition: Selected ion monitoring is mass spectrometry where the abundances of ions of one or more specific m/z values are recorded rather than the entire mass spectrum. [IUPAC]

mass spectrometry scan
type: Class
subclass of: AFP_0001146
definition: A mass spectrometry scan is a scan in a mass spectrometry run. [Allotrope]

multiple reaction monitoring
type: Class
subclass of: selected reaction monitoring
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: MRM
definition: Multiple reaction monitoring is a selected reaction monitoring applied to multiple product ions from one or more precursor ions. [IUPAC]
note: This term should not be confused with consecutive reaction monitoring, which involves the serial application of three or more stages of selected reaction monitoring. [IUPAC]

spray ionization
type: Class
subclass of: AFP_0001993
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
definition: Spray ionization is a ionization that involve dispersing the liquid into fine droplets as a component step. [IUPAC]
note: Most of these techniques are examples of atmospheric pressure ionization. [IUPAC]

ion selection
type: Class
subclass of: AFP_0003335
source: Mass selection
alternative label: mass analysis
alternative label: mass selection
definition: Ion selection is dividing ions according to their mass to charge ratio in a mass analyzer. [Allotrope]

single quadrupole mass spectrometry
type: Class
subclass of: quadrupole mass spectrometry
alternative label: SQDMS
definition: Single quadrupole mass spectrometry is a quadrupole mass spectrometry using a single quadrupole mass analyzer. [Allotrope]

charge deconvolution
type: Class
subclass of: AFP_0003598
AFX_0002808: MS_1000034
definition: Charge deconvolution is a data transformation of a spectrum representing multiply charged ions to singly charged or neutral masses. [Allotrope]

laser desorption ionization
type: Class
subclass of: AFP_0001993
AFX_0002808: CHMO_0002335
alternative label: LDI
definition: A laser desorption ionization is a ionization involving the use of a pulsed laser to induce desorption and ionization of a sample. [Allotrope]

matrix-assisted laser desorption ionization
type: Class
subclass of: laser desorption ionization
AFX_0002808: CHMO_0002334
alternative label: MALDI
alternative label: matrix assisted laser desorption ionization
definition: A matrix-assisted laser desorption ionization is a laser desorption ionization using a laser energy absorbing matrix compound mixed with the sample. [Allotrope]

fragmentation
type: Class
subclass of: AFP_0003712
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
definition: A fragmentation is an ion reaction in which the breakdown of a radical ion forms an ion of lower molar mass and a radical. [IUPAC]

ionization polarity
type: Class
equivalent class: Class
  union of: negative ionization polarity
  union of: positive ionization polarity
  union of: alternating ionization polarity
subclass of: AFQ_0000036
subclass of: Restriction
  on property: RO_0000080
  some values from: AFE_0000004
definition: Ionization polarity is a device configuration of a ionization source whether the ions charge is negative or positive. [Allotrope]

negative ionization polarity
type: Class
subclass of: ionization polarity
alternative label: negative polarity
definition: Polarity of the ionization is negative. [Allotrope]

positive ionization polarity
type: Class
subclass of: ionization polarity
alternative label: positive polarity
definition: Polarity of the ionization is positive. [Allotrope]

alternating ionization polarity
type: Class
subclass of: ionization polarity
alternative label: alternating polarity
definition: Polarity of the ionization is alternating between positive and negative. [Allotrope]

mass spectrometry system configuration
type: Class
subclass of: AFQ_0000036
subclass of: Restriction
  on property: RO_0000080
  some values from: mass spectrometry system
definition: A mass spectrometry system configuration is a device configuration of a mass spectrometry system, that influences the operation of the system. [Allotrope]

SIM spectrum
type: Class
subclass of: AFR_0000439
alternative label: MIM spectrum
alternative label: multiple ion monitoring spectrum
alternative label: selected ion monitoring spectrum
definition: 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]

extracted ion profile
type: Class
subclass of: ion profile
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: extracted ion signal
definition: Any plot of signal intensity observed at a chosen m/z value or set of values in a series of mass spectra recorded as a function of time, including extracted ion chromatogram, extracted ion electropherogram, or from flow injection analysis or any other time-dependent sampling. [IUPAC]

isotope cluster
type: Class
subclass of: AFR_0000231
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
definition: Group of peaks representing ions of the same elemental composition, but different isotopic compositions. [IUPAC]

mass spectrometry tune file
type: Class
subclass of: AFR_0000639
definition: A tune file is a file that contains the tuning parameters of a mass spectrometer tuning. [Allotrope]

multiple reaction monitoring transition report
type: Class
subclass of: IAO_0000088
subclass of: Restriction
  on property: AFX_0002734
  some values from: multiple reaction monitoring
alternative label: MRM transition report
definition: A multiple reaction monitoring (MRM) transition report is a report that is summarizing the analysis of a MRM experiment. [Allotrope]

ion transition
type: Class
subclass of: AFR_0000922
AFX_0002808: MS_1000908
alternative label: multiple reaction monitoring transition
alternative label: transition
definition: An ion transition is a description of the transition from precursor ion to product ions. [Allotrope]
scope note: A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely. [PSI/MS]

ion transition list
type: Class
subclass of: AFR_0000922
subclass of: Class
  intersection of: AFC_0000166
  intersection of: Restriction
    on property: RO_0002351
    some values from: ion transition
AFX_0002798: true
alternative label: transition list
definition: A ion transition list is a collection of ion transitions. [Allotrope]

mass resolution
type: Class
subclass of: AFR_0001619
AFX_0002808: MS_1000011
license: iupac-license
rights: iupac-copyright
source: G. L. Glish, D. J. Burinsky. J. Am. Soc. Mass Spectrom. 19, 161 (2008).
source: IUPAC. Analytical Division. Compendium of Analytical Nomenclature (the Orange Book). Definitive Rules, 1979. Compiled by J. Inczédy, T. Lengyel, A. M. Ure. Blackwell Scientific Publications, Oxford (1997)
source: IUPAC. Compendium of Chemical Terminology, 2nd ed. (the Gold Book). Compiled by A. D. McNaught and A.Wilkinson. Blackwell Scientific Publications, Oxford (1997).
source: J. Laskin, J. H. Futrell. Mass Spectrom. Rev. 24, 135 (2005).
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
definition: Mass resolution is a resolution in a mass spectrum, the observed m/z value divided by the smallest difference Δ(m/z) for two ions that can be separated: (m/z)/Δ(m/z). [IUPAC]

mass spectrometry system setting
type: Class
subclass of: AFR_0001505
definition: A mass spectrometry system setting is a setting that specifies the operation of a mass spectrometry system. [Allotrope]

dwell time
type: Class
subclass of: mass spectrometry system setting
AFX_0002808: MS_1000502
definition: The dwell time is a mass spectrometry system setting that specifies the time spent gathering data across a peak. [Allotrope]

m/z
type: Class
subclass of: AFR_0001583
subclass of: Restriction
  on property: AFX_0002816
  some values from: AFQ_0000257
AFX_0002808: MS_1000040
license: iupac-license
rights: iupac-copyright
alternative label: mass-to-charge ratio
definition: A quantification facet that quantifies the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). [IUPAC]
scope note: Mass-to-charge ratio is deprecated. Mass-to-charge ratio has been used occasionally for the horizontal axis in a plot of a mass spectrum, although the quantity measured is not the ion's mass divided by its electric charge (SI units kg C-1). [IUPAC]
scope note: m/z is recommended as an abbreviation to represent the dimensionless quantity that is used almost universally as the independent variable in a mass spectrum. [IUPAC]

qualifier transition ratio
type: Class
subclass of: AFR_0001101
subclass of: Restriction
  on property: AFX_0002730
  some values from: AFRL_0000312
definition: A qualifier transition ratio is a ratio of the magnitudes of the qualifier transition signal to the quantifier transition signal. [Allotrope]

measured qualifier transition ratio
type: Class
subclass of: qualifier transition ratio
subclass of: AFRL_0000157
definition: A measured qualifier transition ratio is a qualifier transition ratio that has the contextual role of a measure. [Allotrope]

expected qualifier transition ratio
type: Class
subclass of: qualifier transition ratio
subclass of: Restriction
  on property: AFX_0002730
  some values from: AFRL_0000474
definition: An expected qualifier transition ratio is a qualifier transition ratio that has the contextual role of an expected datum. [Allotrope]

minimum qualifier transition ratio
type: Class
subclass of: qualifier transition ratio
subclass of: Restriction
  on property: AFX_0002730
  some values from: AFRL_0000064
definition: A minimum qualifier transition ratio is a qualifier transition ratio that species a minimum allowed qualified transition ratio. [Allotrope]

maximum qualifier transition ratio
type: Class
subclass of: qualifier transition ratio
subclass of: Restriction
  on property: AFX_0002730
  some values from: AFRL_0000064
definition: A maximum qualifier transition ratio is a qualifier transition ratio that species a maximum allowed qualified transition ratio. [Allotrope]

transition qualification
type: Class
subclass of: AFR_0001871
definition: A transition qualification is a qualification that a measured transition ratio that is consistent with the expected transition ratio. [Allotrope]

collision energy
type: Class
subclass of: AFR_0001583
subclass of: Restriction
  on property: AFX_0002816
  some values from: Class
    intersection of: AFQ_0000253
    intersection of: Restriction
      on property: RO_0000080
      some values from: collision energy (material entity)
definition: Collision energy is a quality quantification facet that quantifies the energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. [PSI/MS]

pause time
type: Class
subclass of: mass spectrometry system setting
definition: Pause time is a mass spectrometry system setting that specifies the time in between different ms event's measurement time to allow the instrument to equilibrate. [Allotrope]
scope note: Pause time applies to MRM or SIM events and does not apply to polarity switching time. [Allotrope]

ionization switch delay setting
type: Class
subclass of: AFR_0001243
subclass of: mass spectrometry system setting
subclass of: AFR_0001967
alternative label: ionization switch delay
change note: 2020-01-06 Fix super class. [Allotrope]
definition: A setting that controls the duration of time after which an ion source switches polarity of ionization. [Allotrope]

polarity switch delay setting
type: Class
subclass of: AFR_0001243
subclass of: mass spectrometry system setting
subclass of: AFR_0001967
alternative label: polarity switch delay
change note: 2020-01-06 Fix super class. [Allotrope]
definition: A setting that controls the duration of time after which polarity of a scan switches. [Allotrope]

m/z setting
type: Class
subclass of: AFR_0001243
subclass of: mass spectrometry system setting
alternative label: SIM mass setting
alternative label: mass per charge setting
alternative label: mass setting
alternative label: mass to charge setting
alternative label: selected ion monitoring mass
definition: A m/z is a setting that controls the mass per charge ratio of a scan. [Allotrope]

pre-peak background time measurement datum
type: Class
subclass of: AFR_0000966
AFX_0002798: true
alternative label: pre-peak background time measurement range
definition: Pre-peak background time measurement datum is a time datum that describes the period of time for background correction before a peak is detected. [Allotrope]

post-peak background time measurement datum
type: Class
subclass of: AFR_0000966
AFX_0002798: true
alternative label: post-peak background time measurement range
definition: Post-peak background time measurement datum is a time datum that describes the period of time for background correction after a peak is detected. [Allotrope]

mass spectrometry document
type: Class
subclass of: IAO_0000310
subclass of: Restriction
  on property: IAO_0000136
  some values from: AFP_0001427
alternative label: mass spectrometry result
definition: A mass spectrometry document is a document that encompasses the information associated with a mass spectrometry run. [Allotrope]

total ion profile
type: Class
subclass of: ion profile
AFX_0002808: MS_1000235
alternative label: total ion signal
definition: A total ion profile is an ion profile that is the sum of all detected ion current signals at each time point. [Allotrope]

mass output setting
type: Class
subclass of: AFR_0001696
AFX_0002808: MS_1000502
definition: A mass output setting is a data processing setting that specifies the charge output value on some charge deconvolution output. [Allotrope]

ion profile
type: Class
subclass of: AFR_0001060
alternative label: ion signal
definition: An ion profile is a distribution function of a ion current signal of a mass detector. [Allotrope]

selected ion profile
type: Class
subclass of: ion profile
AFX_0002808: MS_1000627
alternative label: selected ion signal
definition: A selected ion profile is an ion profile where only preselected m/z values are detected in the analysis. [Allotrope]

mass resolution setting
type: Class
subclass of: AFR_0001243
AFX_0002808: MS_1000502
definition: A mass resolution setting is a control setting that specifies the nominal mass resolution target for a mass spectrometry scan. [Allotrope]

ion current signal
type: Class
subclass of: AFR_0002546
definition: An ion current signal is the output of a mass detector, that signals the ion current. [Allotrope]

mass spectrometry aggregate document
type: Class
subclass of: AFC_0000160
subclass of: IAO_0000310
subclass of: Restriction
  on property: RO_0002351
  some values from: mass spectrometry document
definition: A mass spectrometry aggregate document is a document that aggregates mass spectrometry documents. [Allotrope]

m/z minimum setting
type: Class
subclass of: m/z setting
subclass of: Restriction
  on property: AFX_0002704
  some values from: AFR_0002440
alternative label: SIM mass minimum setting
alternative label: mass minimum setting
alternative label: mass per charge minimum setting
alternative label: mass to charge minimum setting
alternative label: selected ion monitoring minimum mass
definition: A m/z minimum setting is a m/z setting that specifies the minimum mass per charge ratio of a scan. [Allotrope]

m/z maximum setting
type: Class
subclass of: m/z setting
subclass of: Restriction
  on property: AFX_0002704
  some values from: AFR_0002441
alternative label: SIM mass maximum setting
alternative label: mass maximum setting
alternative label: mass per charge maximum setting
alternative label: mass to charge maximum setting
alternative label: selected ion monitoring maximum mass
definition: A m/z maximum setting is a m/z setting that specifies the maximum mass per charge ratio of a scan. [Allotrope]

mass spectrum data cube
type: Class
subclass of: AFR_0000992
subclass of: AFR_0002256
subclass of: DataSet
subclass of: Restriction
  on property:
    inverse of: AFX_0002737
  some values from: AFR_0000439
definition: A mass spectrum data cube is a data cube that is a representation of a mass spectrum. [Allotrope]

three-dimensional mass spectrum data cube
type: Class
subclass of: AFR_0000992
subclass of: AFR_0002256
subclass of: DataSet
subclass of: Restriction
  on property:
    inverse of: AFX_0002737
  some values from: AFR_0001950
alternative label: 3 dimensional mass spectrum data cube
alternative label: 3-D mass spectrum data cube
alternative label: 3-dimensional mass spectrum data cube
alternative label: 3D mass spectrum data cube
alternative label: three dimensional mass spectrum data cube
definition: A three-dimensional mass spectrum data cube is a data cube that is a representation of a three-dimensional mass spectrum. [Allotrope]

mass spectrum identifier
type: Class
subclass of: AFR_0000917
subclass of: Restriction
  on property: AFX_0002717
  some values from: AFR_0000439
definition: A mass spectrum identifier is an identifier that identifies some mass spectrum. [Allotrope]

fragmentation aggregate document
type: Class
subclass of: AFC_0000160
subclass of: IAO_0000310
subclass of: Restriction
  on property: RO_0002351
  some values from: fragmentation document
definition: A fragmentation aggregate document is a document that aggregates fragmentation documents. [Allotrope]

fragmentation document
type: Class
subclass of: IAO_0000310
subclass of: Restriction
  on property: IAO_0000136
  some values from: fragmentation
definition: A fragmentation document is a document that encompasses the information associated with some fragmentation. [Allotrope]

isolation window lower limit
type: Class
subclass of: AFR_0001583
definition: An isolation window lower limit is a quality quantification facet that describes the lower limit on the isolation window of some mass spectrometry scan. [Allotrope]

isolation window upper limit
type: Class
subclass of: AFR_0001583
definition: An isolation window upper limit is a quality quantification facet that describes the upper limit on the isolation window of some mass spectrometry scan. [Allotrope]

precursor ion aggregate document
type: Class
subclass of: AFC_0000160
subclass of: IAO_0000310
subclass of: Restriction
  on property: RO_0002351
  some values from: precursor ion document
definition: A precursor ion aggregate document is a document that aggregates precursor ion documents. [Allotrope]

precursor ion document
type: Class
subclass of: IAO_0000310
subclass of: Restriction
  on property: IAO_0000136
  some values from: Class
    intersection of: AFM_0000077
    intersection of: Restriction
      on property: RO_0000087
      some values from: precursor ion role
definition: A precursor ion document is a document that encompasses the information associated with some precursor ion. [Allotrope]

isolation window
type: Class
subclass of: AFR_0001583
definition: An isolation window is a quality quantification facet that describes a range of m/z values which is filtered in a mass spectrometry run to examine some ion of interest via fragmentation. [Allotrope]

mass spectrum level
type: Class
subclass of: AFR_0000984
definition: A mass spectrum level is a count of the current stage in a multiple-stage mass spectrometry process. [Allotrope]

mass spectrometry role
type: Class
equivalent class: Class
  intersection of: BFO_0000023
  intersection of: Restriction
    on property: BFO_0000054
    some values from: AFP_0001427
subclass of: AFRL_0000499
AFX_0002798: true
definition: A mass spectrometry role is a role that is realized in mass spectrometry. [Allotrope]

product ion role
type: Class
subclass of: mass spectrometry role
subclass of: AFRL_0000499
subclass of: Restriction
  on property: RO_0000081
  some values from: Class
    intersection of: AFM_0000077
    intersection of: Restriction
      on property: AFX_0002735
      some values from: Class
        intersection of: BFO_0000015
        intersection of: Restriction
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: product
alternative label: product ion
definition: Ion formed as the product of a reaction involving a particular precursor ion. [IUPAC]

precursor ion role
type: Class
subclass of: mass spectrometry role
subclass of: AFRL_0000499
subclass of: Restriction
  on property: RO_0000081
  some values from: Class
    intersection of: AFM_0000077
    intersection of: Restriction
      on property: AFX_0000554
      some values from: Class
        intersection of: BFO_0000015
        intersection of: Restriction
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: precursor
alternative label: precursor ion
alternative label: precursor role
alternative label: progenitor
alternative label: progenitor ion
alternative label: progenitor ion role
definition: Precursor ion role is a role in mass spectrometry inhered in an ion that reacts to form particular product ions or undergoes specified neutral losses. The reaction can be of different types including unimolecular dissociation, ion/molecule reaction, change in charge state, possibly preceded by isomerization. [IUPAC]

qualifier transition role
type: Class
subclass of: AFRL_0000166
subclass of: Restriction
  on property: AFX_0002726
  some values from: ion transition
alternative label: qualifier transition
definition: A qualifier transition is the contextual role of an ion transition which when compared to the quantifier transition is used to determine the validity of the result. [Allotrope]

quantifier transition role
type: Class
subclass of: AFRL_0000166
subclass of: Restriction
  on property: AFX_0002726
  some values from: ion transition
alternative label: quantifier transition
definition: A quantifier transition is the contextual of an ion transition, that is used to calculate the measured result. [Allotrope]

qualified transition role
type: Class
subclass of: AFRL_0000166
alternative label: qualified transition
definition: Qualified transition role is the contextual role of an ion transition that asserts that the transition meets some qualification requirements. [Allotrope]

reagent role (ms)
type: Class
subclass of: AFRL_0000085
subclass of: mass spectrometry role
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: chemical ionization reagent gas
alternative label: reagent role
definition: Reagent role is the role of a gas that reacts with ions to produce product ions through ion/molecule reactions; for example, a gas such as methane, ammonia, or isobutane used in chemical ionization to create reagent ions or a gas used in ion traps or collision cells to perform gas-phase ion/molecule reactions. [IUPAC]

adduct ion role
type: Class
subclass of: mass spectrometry role
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: adduct
alternative label: adduct ion
alternative label: adduct role
definition: Adduct ion role is the role of an ion formed by the interaction of a precursor 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. [IUPAC]
example: For example, a Na+ adduct of a molecule (M) that is represented as [M + Na]+.

fragment ion role
type: Class
subclass of: product ion role
license: iupac-license
rights: iupac-copyright
source: K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
alternative label: fragment
alternative label: fragment ion
definition: A fragment ion role is a product ion role of an ion that results from the dissociation of a precursor ion. [IUPAC]

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type: Organization

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description: These taxonomies contain material or may constitute derivative works of material which may be subject to copyright by one of the following organizations. By using these taxonomies, you agree to the following terms and conditions applicable to its contents: ****************************************************************************** Copyright Notice and Terms for IUPAC Gold Book ______________________________________________________________________________ Copyright © 1998, Regents of the University of California All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ****************************************************************************** Copyright Notice and Terms for PSI-MS (Proteomics Standards Initiative - Mass Spectrometry) Mass spectrometer output files and spectra interpretati…

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Creative Commons Attribution 4.0 International Public License
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description: Copyright (c) 2019 International Union of Pure Applied Chemistry

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description: Reproduced by permission of International Union of Pure and Applied Chemistry

mass (quality)
change note: 2019-09-09 Changed pref label for uniqueness. [Allotrope]