AFO Mass Spectrometry Domain Ontology (REC/2026/06)
K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609
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]
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]
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]
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]
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]
A. G. Marshall, C. L. Hendrickson, G. S. Jackson. Mass Spectrom. Rev. 17, 1 (1998).
J. P. Holder, L. Gruber, H. E. DeWitt, B. R. Beck, D. A. Church, D. Schneider. Phys. Scr., T 92, 158 (2001).
A ion trap is a device for spatially confining ions using electric and magnetic fields alone or in combination. [IUPAC]
Inlet used for introducing the liquid sample into an electrospray ionization source. [PSI/MS]
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]
An ion source inlet is an inlet into an ion source of a mass spectrometer. [Allotrope]
A single quadrupole mass spectrometer is a type of quadrupole mass spectrometer that uses one single quadrupole field. [Allotrope]
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]
A mass spectrometry system is a measuring system that is designed and assembled to realize the measurement function by way of mass spectrometry. [Allotrope]
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]
A filament is a device that produces an electron stream to charge neutrals for analysis by mass spectrometry. [Allotrope]
Collision energy is energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. [PSI/MS]
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]
This term is not synonymous with chemi-ionization. [IUPAC]
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]
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 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 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]
E. de Hoffmann (1996). Tandem Mass Spectrometry: a Primer. Journal of Mass Spectrometry 31: 129–137.
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]
Selected reaction monitoring applied to multiple product ions from one or more precursor ions is known as multiple reaction monitoring. [IUPAC]
Selected reaction monitoring in multiple-stage mass spectrometry is known as consecutive reaction monitoring. [IUPAC]
J. B. Fenn, M. Mann, C. K. Meng, S. F. Wong, C. M. Whitehouse. Science 246, 64 (1989).
M. Dole, L. L. Mack, R. L. Hines, R. C. Mobley, L. D. Ferguson, M. B. Alice. J. Chem. Phys. 49, 2240 (1968).
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]
The term ionspray is deprecated unless describing the commercial product.
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]
A mass spectrometry scan is a scan in a mass spectrometry run. [Allotrope]
Multiple reaction monitoring is a selected reaction monitoring applied to multiple product ions from one or more precursor ions. [IUPAC]
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 is a ionization that involve dispersing the liquid into fine droplets as a component step. [IUPAC]
Most of these techniques are examples of atmospheric pressure ionization. [IUPAC]
Ion selection is dividing ions according to their mass to charge ratio in a mass analyzer. [Allotrope]
Single quadrupole mass spectrometry is a quadrupole mass spectrometry using a single quadrupole mass analyzer. [Allotrope]
Charge deconvolution is a data transformation of a spectrum representing multiply charged ions to singly charged or neutral masses. [Allotrope]
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
A matrix-assisted laser desorption ionization is a laser desorption ionization using a laser energy absorbing matrix compound mixed with the sample. [Allotrope]
matrix-assisted laser desorption ionization
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 is a device configuration of a ionization source whether the ions charge is negative or positive. [Allotrope]
Polarity of the ionization is negative. [Allotrope]
Polarity of the ionization is positive. [Allotrope]
Polarity of the ionization is alternating between positive and negative. [Allotrope]
A mass spectrometry system configuration is a device configuration of a mass spectrometry system, that influences the operation of the system. [Allotrope]
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]
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]
Group of peaks representing ions of the same elemental composition, but different isotopic compositions. [IUPAC]
A tune file is a file that contains the tuning parameters of a mass spectrometer tuning. [Allotrope]
A multiple reaction monitoring (MRM) transition report is a report that is summarizing the analysis of a MRM experiment. [Allotrope]
multiple reaction monitoring transition report
An ion transition is a description of the transition from precursor ion to product ions. [Allotrope]
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]
A ion transition list is a collection of ion transitions. [Allotrope]
G. L. Glish, D. J. Burinsky. J. Am. Soc. Mass Spectrom. 19, 161 (2008).
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)
IUPAC. Compendium of Chemical Terminology, 2nd ed. (the Gold Book). Compiled by A. D. McNaught and A.Wilkinson. Blackwell Scientific Publications, Oxford (1997).
J. Laskin, J. H. Futrell. Mass Spectrom. Rev. 24, 135 (2005).
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]
A mass spectrometry system setting is a setting that specifies the operation of a mass spectrometry system. [Allotrope]
The dwell time is a mass spectrometry system setting that specifies the time spent gathering data across a peak. [Allotrope]
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]
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]
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]
A qualifier transition ratio is a ratio of the magnitudes of the qualifier transition signal to the quantifier transition signal. [Allotrope]
A measured qualifier transition ratio is a qualifier transition ratio that has the contextual role of a measure. [Allotrope]
An expected qualifier transition ratio is a qualifier transition ratio that has the contextual role of an expected datum. [Allotrope]
A minimum qualifier transition ratio is a qualifier transition ratio that species a minimum allowed qualified transition ratio. [Allotrope]
A maximum qualifier transition ratio is a qualifier transition ratio that species a maximum allowed qualified transition ratio. [Allotrope]
A transition qualification is a qualification that a measured transition ratio that is consistent with the expected transition ratio. [Allotrope]
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 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]
Pause time applies to MRM or SIM events and does not apply to polarity switching time. [Allotrope]
A setting that controls the duration of time after which an ion source switches polarity of ionization. [Allotrope]
A setting that controls the duration of time after which polarity of a scan switches. [Allotrope]
A m/z is a setting that controls the mass per charge ratio of a scan. [Allotrope]
pre-peak background time measurement range
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]
pre-peak background time measurement datum
post-peak background time measurement range
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]
post-peak background time measurement datum
A mass spectrometry document is a document that encompasses the information associated with a mass spectrometry run. [Allotrope]
A total ion profile is an ion profile that is the sum of all detected ion current signals at each time point. [Allotrope]
A mass output setting is a data processing setting that specifies the charge output value on some charge deconvolution output. [Allotrope]
An ion profile is a distribution function of a ion current signal of a mass detector. [Allotrope]
A selected ion profile is an ion profile where only preselected m/z values are detected in the analysis. [Allotrope]
A mass resolution setting is a control setting that specifies the nominal mass resolution target for a mass spectrometry scan. [Allotrope]
An ion current signal is the output of a mass detector, that signals the ion current. [Allotrope]
A mass spectrometry aggregate document is a document that aggregates mass spectrometry documents. [Allotrope]
A m/z minimum setting is a m/z setting that specifies the minimum mass per charge ratio of a scan. [Allotrope]
A m/z maximum setting is a m/z setting that specifies the maximum mass per charge ratio of a scan. [Allotrope]
A mass spectrum data cube is a data cube that is a representation of a mass spectrum. [Allotrope]
three dimensional mass spectrum data cube
A three-dimensional mass spectrum data cube is a data cube that is a representation of a three-dimensional mass spectrum. [Allotrope]
three-dimensional mass spectrum data cube
A mass spectrum identifier is an identifier that identifies some mass spectrum. [Allotrope]
A fragmentation aggregate document is a document that aggregates fragmentation documents. [Allotrope]
A fragmentation document is a document that encompasses the information associated with some fragmentation. [Allotrope]
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]
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]
A precursor ion aggregate document is a document that aggregates precursor ion documents. [Allotrope]
A precursor ion document is a document that encompasses the information associated with some precursor ion. [Allotrope]
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]
A mass spectrum level is a count of the current stage in a multiple-stage mass spectrometry process. [Allotrope]
A mass spectrometry role is a role that is realized in mass spectrometry. [Allotrope]
Ion formed as the product of a reaction involving a particular precursor ion. [IUPAC]
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]
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]
A quantifier transition is the contextual of an ion transition, that is used to calculate the measured result. [Allotrope]
Qualified transition role is the contextual role of an ion transition that asserts that the transition meets some qualification requirements. [Allotrope]
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 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]
For example, a Na+ adduct of a molecule (M) that is represented as [M + Na]+.
A fragment ion role is a product ion role of an ion that results from the dissociation of a precursor ion. [IUPAC]
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 interpretation _____________________________________________________________________________ Created by Matt Chambers, Andreas Bertsch, Marius Kallhardt, Eric Deutsch Fredrik Levander, Pierre-Alain Binz, and Gerhard Mayer. Publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group. This work is used pursuant to a Creative Commons license available here: http://creativecommons.org/licenses/by/3.0/legalcode ****************************************************************************** Attribution Notice for National Center for Biomedical Ontology materials. This work contains material from the Cell Ontology and Clinical Measurement Ontology, available here: http://bioportal.bioontology.org/. ****************************************************************************** Attribution Notice for ChEBI This work contains material from the European Bioinformatics Institute’s ChEBI database. ****************************************************************************** Attribution Notice for Quantities Units Dimensions Data Types (http://www.qudt.org/) This work contains content from www.qudt.org and is used pursuant to a Creative Commons License available here: http://creativecommons.org/licenses/by-sa/3.0/us/legalcode. The original work may have been modified. ****************************************************************************** Copyright and Attribution Notice for Dublin Core Metadata Initiative Document This work contains material from the following DCMI document used pursuant to a creative commons license available here: https://creativecommons.org/licenses/by/4.0/legalcode. This material may have been modified or changed. Timestamped URL: http://dublincore.org/documents/2012/06/14/dcmi-terms/ Date Issued: 2012-06-14 Document Status: This is a DCMI Recommendation. Copyright © 1995-2015 DCMI. All Rights Reserved. DCMI liability, trademark/service mark, document use and software licensing rules apply. ******************************************************************************
Copyright © 2015-2026 Allotrope Foundation
This work is licensed under a Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/. THESE MATERIALS ARE PROVIDED "AS IS" AND ALLOTROPE EXPRESSLY DISCLAIMS ALL WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, TITLE, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. Copyright © 2015-2026 Allotrope Foundation
Creative Commons Attribution 4.0 International Public License
Copyright (c) 2019 International Union of Pure Applied Chemistry
Reproduced by permission of International Union of Pure and Applied Chemistry
2019-09-09 Changed pref label for uniqueness. [Allotrope]