Mass Spectrometry Terms and Definitions


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. 

collisionally activated dissociation (CAD)

Dissociation of an ion after collisional excitation.

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

Resolving power (in mass spectrometry)

Measure of the ability of a mass spectrometer to provide a specified value of mass resolution.

Note: The procedure by which Δ(m/z) was defined and measured, and the m/z value at which the measurement was made, should be reported.


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).

Note 1: The m/z value at which the measurement was made should be reported.

Note 2: The definition and method of measurement of Δ(m/z) should be reported. Commonly this is performed using peak width measured at a specified percentage of peak height.

Note 3: Alternatively Δ(m/z) is defined as the separation between two adjacent equal magnitude peaks such that the valley between them is a specified fraction of the peak height, for example as measured by peak matching.

Electrospray ionization

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.

Note: 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 ionspray is deprecated unless describing the commercial product.

extracted ion chromatogram

AKA: mass chromatogramreconstructed ion chromatogram

Chromatogram created by plotting the intensity of the signal observed at a chosen m/z value or set of values in a series of mass spectra recorded as a function of retention time.

Stable isotope labeling 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.

Tandem Mass Tags (TMT) and Isobaric tag for relative and absolute quantitation (iTRAQ)

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.

Label-free quantification (LFQ)

Method of determining the concentration of proteins through a combination of protein digestion and LC/MS without relying on stable isotope labeling. Protein quantification is achieved by measuring the signal intensity of peptide ions corresponding to a protein or by counting and comparing the number of fragment mass spectra identifying peptides of a given protein.

Shotgun proteomics

Protein identification using a combination of high-performance liquid chromatography and mass spectrometry in which the proteins in a mixture are digested, usually by a specific enzyme, and the resulting peptides are separated by liquid chromatography and identified by tandem mass spectrometry.

Selected reaction monitoring (SRM) and multiple reaction monitoring (MRM)

A two-stage targeted analysis strategy in which a precursor ion is selected and fragmented and the intensity of a selected fragment ion is measured. Each pair of precursor and fragment ions constitutes a single assay. Determination of the fragments and instrument parameters are identified empirically to maximize sensitivity and selectivity.