MS Terms

A short list of terms and definitions for mass spectrometry as recommended by IUPAC

(from K. K. Murray et al., Pure Appl. Chem., 2013, Vol. 85, No. 7, pp. 1515-1609)

Accurate mass

Experimentally determined mass of an ion of known charge.
Can be used to determine elemental composition to within limits defined by both the accuracy and precision of the measurement.
Accurate mass and exact mass are not synonymous. Accurate mass refers to a measured mass, and exact mass refers to a calculated mass.
See also exact mass.

AQUA – absolute quantitation of proteins

Method for absolute quantitation of proteins through measurements on constituent proteolytic peptides using chemically synthesized isotope-labeled peptides as surrogate internal standards for mass spectrometry.

API – atmospheric pressure ionization

Ionization process in which ions are formed from atoms or molecules at atmospheric pressure.

Note: Atmospheric pressure ionization is not a synonym for atmospheric pressure chemical ionization.

APCI – atmospheric pressure chemical ionization

Chemical ionization of a sample that is a gas or nebulized liquid, using an atmospheric pressure corona discharge or beta emitter such as 63Ni.

CID (and CAD) collision-induced dissociation (and collisionally activated dissociation)

Dissociation of an ion after collisional excitation.

Note: The terms collision-induced dissociation (CID) and collisionally activated dissociation (CAD) can be used interchangeably.

CRM – consecutive reaction monitoring

Multiple-stage mass spectrometry experiment with three or more stages of m/z separation in which products of sequential fragmentation or bimolecular reactions are selected for detection. See also multiple reaction monitoring.

DDA – data-dependent acquisition

Mode of data collection in tandem mass spectrometry in which a fixed number of precursor ions whose m/z values were recorded in a survey scan are selected using predetermined rules and are subjected to a second stage of mass selection in an MS/MS analysis.

DE – dynamic exclusion

Software method used to minimize repeat selections of identical precursor ions for collision-induced dissociation in replicate chromatography-tandem mass spectrometry analyses of complex mixtures. See also data-dependent acquisition.

ECD – electron capture dissociation

Process in which multiply protonated molecules interact with low-energy electrons followed by fragmentation. The capture of an electron by the even-electron cation [M + nH]n+ liberates energy and reduces its charge state, thus producing the corresponding [M + nH](n–1)+• odd-electron ion, which readily fragments.

ETD – electron transfer dissociation

Process in which multiply protonated molecules accept an electron from an anion with relatively low electron affinity. Capture of the electron leads to the liberation of energy and a reduction in charge of the ion with the production of the [M + nH](n–1)+• odd-electron ion, which is readily fragmented by collision-induced dissociation. See also electron capture dissociation (ECD)

ESI – electrospray ionization

Spray ionization process in which either cations or anions in solution are transferred to the gas phase through 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.

Exact mass

Calculated mass of an ion or molecule with specified isotopic composition.
See also accurate mass.

FTMS – Fourier transform mass spectrometry

Mass spectrometry technique in which m/z values are represented by frequencies of ion motion and mass spectra are generated by Fourier transform mathematical operations from time domain transients produced by image current detection.

Note: Fourier transform mass spectrometry is typically carried out using Fourier transform ion cyclotron resonance-mass spectrometers or Kingdon traps (e.g. Orbitraps).

GC-MS (or GC/MS) gas chromatography-mass spectrometry (or gas chromatography/mass spectrometry)

Technique by which a mixture is separated into individual components by gas chromatography, followed by detection with a mass spectrometer.

Note 1: Either a hyphen or slash can be used to indicate combined instruments.

Note 2: The mass spectrum is typically obtained on a time scale that allows resolution of the component in a single chromatographic peak.

ICP-MS  – inductively coupled plasma-mass spectrometry

Mass spectrometry technique based on coupling a mass spectrometer with an inductively coupled plasma as an ion source that both atomizes samples into their constituent atoms and ionizes them to form atomic cations.

Note: The technique is highly sensitive for a range of metals and several non-metals, and provides information on isotopic distributions.

IT – ion trap

Device for spatially confining ions using electric and magnetic fields alone or in combination.

iTRAQ – isobaric tag for relative and absolute quantitation

Chemical labeling reagents used for relative or absolute quantitation in proteomics, based on covalent labeling of the N-terminus and side-chain amines of peptides from protein digestions with tags of varying mass.

IDMS – isotope dilution mass spectrometry

Quantitative mass spectrometry technique in which an isotopically enriched compound is used as a surrogate internal standard

IRMS – isotope ratio mass spectrometry, stable isotope mass spectrometry

Measurement and study of the relative abundances of the different isotopes of an element in a material using a mass spectrometer.

Isobar (in mass spectrometry)

Atomic or molecular species with the same nominal mass but different exact masses. Isobaric ions are isobars that all carry an electric charge.

LIT – linear ion trap

Two-dimensional Paul ion trap in which ions are confined in the axial dimension by means of a static electric potential.

LC-MS (or LC/MS) liquid chromatography-mass spectrometry (or liquid chromatography/mass spectrometry)

Technique by which a mixture of analytes is separated into individual components by liquid chromatography (typically high-performance liquid chromatography), followed by detection with a mass spectrometer.

Note: Either a hyphen or slash can be used to indicate combined instruments.

Lock mass

Mass of an ion of known m/z value, derived from a suitable standard compound introduced into an ion source together with the sample to be analyzed, which permits real-time recalibration by correction of m/z shifts arising from instrumental drift.

Monoisotopic mass

Exact mass of an ion or molecule calculated using the mass of the most abundant isotope of each element.

See also accurate mass.

MS – mass spectrometry

Study of matter through the formation of gas-phase ions that are characterized using mass spectrometers by their mass, charge, structure, and/or physico-chemical properties.

Note 1: The term is a misnomer because it is m/z rather than mass that is the independent variable in a mass spectrum.

Note 2: Mass spectroscopy is an obsolete synonym for mass spectrometry that should not be used to avoid confusion with spectroscopies in which the measured quantity is the absorption or emission of electromagnetic radiation.

MS/MS – mass spectrometry/mass spectrometry, tandem mass spectrometry

Acquisition and study of the spectra of the product ions or precursor ions of m/z selected ions, or of precursor ions of a selected neutral mass loss.

Note: MS/MS can be accomplished using instruments incorporating more than one analyzer (tandem mass spectrometry in space) or in trap instruments (tandem mass spectrometry in time).

MS/MS spectrum

Mass spectrum obtained using tandem mass spectrometry.


Symbol for multiple-stage mass spectrometry experiments designed to record product ion spectra where n is the number of product ion stages (n-th-generation product ions).

MudPIT – multidimensional protein identification technology

Variant of shotgun proteomics in which proteins are first digested and then separated by a combination of strong cation exchange and reversed-phase liquid chromatography followed by mass spectrometry detection.

MRM – multiple reaction monitoring

Application of selected reaction monitoring to multiple product ions from one or more precursor ions.

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.


Deprecated: mass-to-charge ratio, thomson. Abbreviation representing the dimensionless quantity formed by dividing the ratio of the mass of an ion to the unified atomic mass unit, by its charge number (regardless of sign). The abbreviation is written in italicized lowercase letters with no spaces.

Note 1: 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). However, 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.

Nominal mass

Mass of a molecular ion or molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element.
See also monoisotopic mass.

QIT – quadrupole ion trap (Paul ion trap, QUISTOR – quadrupole ion storage trap)

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.

QTOF – quadrupole time-of-flight

Hybrid mass spectrometer consisting of a transmission quadrupole mass spectrometer coupled to an orthogonal acceleration time-of-flight mass spectrometer. A collision quadrupole is typically inserted between the two mass spectrometers.

QCAT – quantitation by concatenated tryptic peptides

Method for absolute quantitation of a protein or proteins in a multiplexed fashion using isotope-labeled peptides as surrogate internal standards. The labeled peptides are produced by synthesizing a gene coding for all desired peptides, expressing this gene in E. coli culture containing appropriately labeled substrate, and digesting with trypsin the expressed protein composed of the desired concatenated peptides.

SIM – selected ion monitoring

Operation of a mass spectrometer in which the abundances of ions of one or more specific m/z values are recorded rather than the entire mass spectrum. See also selected reaction monitoring (SRM).

SRM – selected reaction monitoring

Data acquired from one or more specific product ions corresponding to m/z selected precursor ions recorded via two or more stages of mass spectrometry.

SILAC – stable isotope ratio analysis of amino acids in cell culture

Proteomics technique that detects differences in protein abundance between cultured cell samples using stable isotopic labeling achieved with labeled amino acids in one cell culture and unlabeled ones in a separate culture.

SISCAPA – stable isotope standards and capture by anti-peptide antibodies

Method for absolute quantitation of a protein or proteins in a multiplexed fashion using isotope-labeled peptides as surrogate internal standards. The labeled peptides are produced by synthesizing a gene coding for each desired peptide, cell-free transcription, and translation of this gene in a medium containing 13C6-labeled lysine, and digesting with trypsin the expressed protein composed of the desired concatenated peptides. For low-abundance proteins the sensitivity is increased by selective enrichment of the target peptides by antibody capture.

TOF-MS – time-of-flight mass spectrometer

Mass spectrometer that separates ions by m/z in a field-free region after acceleration through a fixed accelerating potential. Ions of the same initial translational energy and different m/z require different times to traverse a given distance in the field-free region.

TIC – total ion current

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.

TICC –  total ion current chromatogram, reconstructed total ion current chromatogram

Deprecated: total ion chromatogram. Chromatogram created by plotting the total ion current in a series of mass spectra recorded as a function of retention time.

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