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Mass spectrometry glossary & taxonomy
 Evolving Terminologies for Emerging Technologies
Comments? Questions? Revisions? 
Mary Chitty MSLS
Last revised January 09, 2020   

Technologies term index   Finding guide to terms in these glossaries  
Related glossaries include  Biomarkers  Chromatography & electrophoresis
, Protein Structure, Proteomics. Structural genomics

2-D CE-IMLS 2D Capillary Electrophoresis with Inverted Mass Ladder Sequencing:  Combination of capillary electrophoresis and mass spectrometry Fluorescence using LIF (Laser Induced Fluorescence) detection to quantify the amount of protein in the sample. Each LIF peak is then subjected to ESI- TOF MS.

accelerator mass spectrometry: differs from other forms of mass spectrometry in that it accelerates ions to extraordinarily high kinetic energies before mass analysis. The special strength of AMS among the mass spectrometric methods is its power to separate a rare isotope from an abundant neighboring mass ("abundance sensitivity", e.g. 14C from 12C).[1] The method suppresses molecular isobars completely and in many cases can separate atomic isobars (e.g. 14N from 14C) also. This makes possible the detection of naturally occurring, long-lived radio-isotopes such as 10Be, 36Cl, 26Al and 14C. Their typical isotopic abundance ranges from 10−12 to 10−18. AMS can outperform the competing technique of decay counting for all isotopes where the half-life is long enough.[2] Wikipedia accessed 2018 Feb 16

affinity mass spectrometry: The coupling of solid- phase affinity methods with direct analysis by MALDI- TOF MS, an approach loosely referred to as "affinity mass spectrometry", has greatly increased the speed and scope of MALDI- TOF MS analysis. Smith, Lloyd et al, Nature Biotechnology 15: 1368 Dec 1997

affinity based biomolecular mass spectrometry: Advances in biomolecular mass spectrometry (Bio-MS) have made this technique an invaluable tool for analytical chemists and biochemists alike. The applicability of Bio- MS approaches in drug discovery now encompasses in vitro, cellular, and in vivo pharmacological and clinical applications in an unprecedented expansion of utility. As a result, the role of Bio- MS in pharmaceutical discovery continues to proliferate for both structural and functional characterization of biomolecules. From target characterization to lead optimization, affinity techniques have been used to purify, probe, and enrich analytes of interest. Affinity selection employed prior to MS analysis can "edit" out extraneous noise and enable the researcher to examine only what is important. These affinity- based methods can be used as an alternative strategy when classical biochemical techniques are insufficient in advancing difficult projects. MA Kelly, TJ McLellan, PJ Rosner, Strategic use of affinity- based mass spectrometry techniques in the drug discovery process, Analytical Chemistry 74(1): 1- 9, Jan. 1,  2002

biomolecular interaction analysis mass spectrometry: A two- dimensional, chip- based, analytical technique for rapid and sensitive analysis of biomolecules. ... represents a synergy of two individual technologies: surface plasmon resonance (SPR) sensing and matrix- assisted laser desorption/ ionization time-of- flight (MALDI- TOF) mass spectrometry. D Nedelkov and RW Nelson "Biomolecular Interaction Analysis Mass Spectrometry: A multiplexed proteomics approach" Biopharm 28- 33, Aug. 2001

bottom-up mass spectrometry: See under top-down mass spectrometry

CE-MS Capillary Electrophoresis Mass Spectrometry. Separation is achieved through channels etched on the surface of the capillary (connected to an external high- voltage power supply) which delivers sample to ESI-MS. Automatable approach, with great sensitivity. 

CIEF Capillary electrophoresis IsoElectric Focusing: Sample is "focused" in the capillary tube, both separating and concentrating the protein or peptide at its isoelectric point. Then the entire mixture is delivered to the mass spectrometer. Using this technique the researchers have been able to record the molecular weight of all the proteins under study. Can be used to separate proteins from microorganisms. 

Collision Induced Dissociation CID: Introduced in 1968 by chemistry professors, Keith R. Jennings of the University of Warwick, England and [Fred] McLafferty, who was then at Purdue University. The combination of the newer soft ionization methods with collision- induced dissociation is what gives tandem MS its power in the analysis of mixtures. S Borman, "A brief history of mass spectrometry instrumentation" May 1998

Collision-induced dissociation (CID) and collisionally activated dissociation (CAD) refer to the process in which a collision between and ion and a neutral species results in the conversion of part of the translational energy into internal energy of the ion and subsequent fragmentation. The IUPAC document defines the two terms equivalently as does Price (JASMS, 2, 336, 1991). The ASMS Terms and Definitions document does not mention CAD. Sparkman defines CAD and CID equivalently, but notes his preference for CAD. A search of the literature for "collision induced dissociation" and "collisionally activated dissociation" suggests that the former term is preferred. In Figure 1, the number of occurrences of the above strings in journal articles is plotted as a function of the year of publication. The plot shows a clear preference for CID over CAD that increases after 1990.  CAD vs. CID MS Terms Wiki 

Desorption/Ionization Mass Spectrometry: J. Wei, J.  Buriak, G. Siuzdak, Desorption/Ionization Mass Spectrometry on Porous Silicon Nature, 399 (6733): 243- 246, 1999

detector: Related terms: ionization source, mass analyzer  See also Labels, Signaling & DetectionUltrasensitivity 

ElectroSpray Ionization Mass Spectrometry ESI: 
In ESI MS, highly charged droplets dispersed from a capillary in an electric field are evaporated, and the resulting ions are drawn into an MS inlet. The technique was first conceived in the 1960’s by chemistry professor Malcolm Dole of Northwestern University, Evanston, but it was put into practice in the early 1980’s by molecular beam researcher John B. Fenn of Yale University (now at the department of chemistry of Virginia Commonwealth University, Richmond). S Borman, "A brief history of mass spectrometry instrumentation" May 1998 Narrower term: nanoelectrospray

A mass spectrometry technique used for analysis of nonvolatile compounds such as proteins and macromolecules. The technique involves preparing electrically charged droplets from analyte molecules dissolved in solvent. The electrically charged droplets enter a vacuum chamber where the solvent is evaporated. Evaporation of solvent reduces the droplet size, thereby increasing the coulombic repulsion within the droplet. As the charged droplets get smaller, the excess charge within them causes them to disintegrate and release analyte molecules. The volatilized analyte molecules are then analyzed by mass spectrometry.  MeSH, 2001

ESI-MS/MS ElectroSpray tandem Mass Spectrometry: Provides better certainty of protein identification, especially when used in combination with MALDI-TOF, because it generates peptide sequence information as well as mass and predictable fragmentation patterns. Can also be used with mixtures of proteins. Fully automated. Identification is achieved by correlating these data with information in sequence databases.

ESI-TOF ElectroSpray Ionization-Time of Flight: Companies such as Sensar, Micromass, and PerSeptive have concluded that conventional ESI can be modified for compatibility with the short pulse requirements of TOF. Orthogonal acceleration ESI- TOF is one promising approach. In this technique, a continuous flow of ions (either from a static source or from a flowing system such as capillary electrophoresis) is gently accelerated in one direction, resulting in a densely packed but slowly moving analyte ion stream. A second acceleration mechanism that pulses at right angles to this ion stream pushes a well- defined packet of ions toward a detector, which can be almost any kind of mass analyzer, including TOF. Bob Sinclair " MALDI- TOF Goes Mainstream" Scientist 13 (12): 18 June 7 1999 

Fast Atom Bombardment Mass Spectrometry FAB/MS: A mass spectrometric technique that is used for the analysis of a wide range of biomolecules, such as glycoalkaloids, glycoproteins, polysaccharides, and peptides. Positive and negative fast atom bombardment spectra are recorded on a mass spectrometer fitted with an atom gun with xenon as the customary beam. The mass spectra obtained contain molecular weight recognition as well as sequence information. MeSH, 1991

FIA/MS: See Flow Injection Analysis

Flow Injection Analysis: The analysis of a chemical substance by inserting a sample into a carrier stream of reagent using a sample injection valve that propels the sample downstream where mixing occurs in a coiled tube, then passes into a flow- through detector and a recorder or other data handling device MeSH, 1992

Gas Chromatography Mass Spectrometry: A microanalytical technique combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds. MeSH 2007 [1976]

hybrid mass spectrometry: See under tandem mass spectrometry. 

hyphenated techniques: Include EST- MS/MS, ESI- TOF, LC/MS, others?

ion trap mass spectrometry: Arrangement in which ions with a desired range of quotients mass/charge are first made to describe stable paths under the effect of a high- frequency electric quadrupole field, and are then separated and presented to a detector by adjusting the field so as to selectively induce path instability according to their respective mass/charge ratios. IUPAC MS Narrower term: quadrupole ion trap

ion trap: See under quadrupole ion trap
ionization source: Related terms: detector, mass analyzer

Liquid Chromatography/ Mass Spectrometry LC/MS: Used for drug screening, pharmacology studies, environmental analyses and forensics.

MALDI Matrix Assisted Laser Desorption Ionization Mass Spectrometry: A mass spectrometric technique that is used for the analysis of large biomolecules. Analyte molecules are embedded in an excess matrix of small organic molecules that show a high resonant absorption at the laser wavelength used. The matrix absorbs the laser energy, thus inducing a soft disintegration of the sample- matrix mixture into free (gas phase) matrix and analyte molecules and molecular ions. In general, only molecular ions of the analyte molecules are produced and almost no fragmentation occurs. This makes the method well suited for molecular weight determinations and mixture analysis. MESH, 1996

A critical step in the mass spectrometric characterization of biological materials (analytes) is the process of desorbing the analyte from a surface or matrix into the vacuum of the mass spectrometer. Laser irradiation of a light- absorbing matrix doped with analyte results in release of molecules into the vacuum of the mass spectrometer. Progress is being made in developing quantitative MALDI mass spectrometric methods. National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999

In MALDI, sample molecules are laser- desorbed from a solid or liquid matrix containing a highly UV- absorbing substance. MALDI MS, a form of laser desorption MS, was developed in 1985 at the University of Frankfurt, Germany by professor of biophysics Franz Hillenkamp (now at the University of Munster, Germany and Michael Karas (now professor of analytical instrumentation at J.W. Goethe University, Frankfurt, and independently by research scientist Koichi Tanaka and coworkers at Shimadzu Corp., Kyoto Japan  S Borman, "A brief history of mass spectrometry instrumentation" May 1998  Narrower terms: MALDI- TOF, MALDI- TOF- PMF

MALDI-TOF Matrix Assisted Laser Desorption Ionization-Time of Flight mass spectrometry: With MALDI-TOF (matrix- assisted laser desorption- ionization time- of- flight) mass spectrometry, a laser beam passes through the substances to be analyzed, and the laser causes these elements to vaporize and their molecules to fly upward into a tube. Time of flight through the tube correlates directly to mass, with lighter molecules having a shorter time of flight than heavier ones.

MALDI (Matrix-Assisted Laser Desorption-Ionization) TOF (Time Of Flight) mass spectrometry DNA sequencing also has promise. The MALDI-TOF mass spectrometer measures the exact mass of DNA fragments and is capable of accurately predicting the sequence of a DNA fragment based on the molecules mass. MALDI (Matrix-Assisted Laser Desorption-Ionization) TOF (Time Of Flight) mass spectrometry DNA sequencing also has promise. ...  The [Sequenom] MALDI-TOF mass spectrometer measures the exact mass of DNA fragments and is capable of accurately predicting the sequence of a DNA fragment based on the molecules mass.  

The concept of TOF MS was proposed in 1946 by William E. Stephens of the University of Pennsylvania. In a TOF analyzer, ions are separated by differences in their velocities as they move in a straight path toward a collector in order of increasing mass- to- charge ratio. TOF MS is fast, it is applicable to chromatographic detection, and it is now used for the determination of large biomolecules. ... Key advances were made by William C. Wiley and I. H. McLaren of Bendix Corp., Detroit MI -  the first company to commercialize TOF mass spectrometers. According to pharmacology professor Robert J. Cotter of Johns Hopkins University School of Medicine, Wiley and McLaren "devised a time- lag focusing scheme that improved mass resolution by simultaneously correcting for the initial spatial and kinetic energy distributions of the ions … When commercial TOF instruments first came out "their performance in resolution was so poor that they never lived up to even single- focusing magnetic instruments," says [Klaus] Biemann. However, he adds, "this analyzer has been greatly improved recently … to almost match the most sophisticated, and very expensive, double- focusing mass spectrometers." . S Borman, "A brief history of mass spectrometry instrumentation" May 1998  Related term: affinity mass spectrometry.

MALDI-TOF/PMF Matrix Assisted Laser Desorption Ionization- Time of Flight / Peptide Mass Fingerprinting: Related term: PMF Protein Mass Fingerprinting

mass analysis: A process by which a mixture of ionic or neutral species is identified according to the mass- to- charge (m/ z) ratios (ions) or their aggregate atomic masses (neutrals). The analysis may be qualitative and/ or quantitative. IUPAC Compendium

mass spectrometers:
 Generally couple three devices: an ionization device, a mass analyzer, and a detector. The most common ionization techniques used in biology are matrix- assisted laser desorption ionization (MALDI) and electrospray ionization (ESI). ... Once a sample has been ionized, it must be mass analyzed. ...  The most commonly used mass analyzers for protein biochemistry applications are time- of- flight (TOF), triple- quadrupole, quadrupole- TOF, and ion trap instruments. Jeffrey Perkel "Mass Spectrometry Applications for Proteomics" Scientist 15[16]:31, Aug. 20, 2001

mass spectrometry MS: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers. MeSH 2007 [1971]

In a typical approach, this technique for measuring and analyzing molecules involves introducing enough energy into a target molecule to cause its disintegration. The resulting fragments are then analyzed, based on their mass/ charge ratios, to produce a "molecular fingerprint."   A significant force behind progress in proteomics.  

Mass spectrometry can identify protein sequences and post translational modifications, helping to figure out protein functions and other useful knowledge for pharmaceutical R & D; Narrower terms: 2D CE-IMLS 2D Capillary Electrophoresis with inverted Mass Ladder Sequencing, CE-MS, ESI, ESI- MS/MS, ESI- TOF, FT, ICR, hybrid mass spectrometry, ion trap mass spectrometry, LC/MS, MALDI, MALDI- TOF, MALDI- TOF/ PMF, MIMS, MS/MS, MS/MS/MS, multiple mass spectrometry, nanoelectrospray- MS/MS, pyrolysis mass spectrometry, quadrupole ion trap, TOF, tandem mass spectrometer, triple quadrupole 

mass spectromtry informatics: Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry.  Wikipedia accessed 2018 Dec 2

mass spectrum analysis: Analysis of the mass of an object through means of determining the wave length(s) at which electromagnetic energy is absorbed by that object. MeSH, 1974

mass-to-charge ratio m/z: The abbreviation m/ z is used to denote the dimensionless quantity formed by dividing the mass number of an ion by its charge number. It has long been called the mass- to- charge ratio although m is not the ionic mass nor is z a multiple or the elementary (electronic) charge e. The abbreviation m/z therefore, is not recommended. IUPAC Compendium

MS/MS scans:
Related term: tandem mass spectrometry.
See multiple mass spectrometry.

Multi-isotope Imaging Mass Spectrometry MIMS: Secondary-ion mass spectrometry (SIMS) is an important tool for investigating isotopic composition in the chemical and materials sciences, but its use in biology has been limited by technical considerations. Multi-isotope imaging mass spectrometry (MIMS), which combines a new generation of SIMS instrument with sophisticated ion optics, labeling with stable isotopes, and quantitative image-analysis software, was developed to study biological materials.  High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry Claude Lechene, Journal of Biology 2006, 5:20doi:10.1186/jbiol42 

multiple mass spectrometry MS/MS/MS: Provides even greater certainty of identification and additional characterization information than electrospray ionization/ tandem mass spectrometry. Fully automated. When more than two stages are involved, the technique is called multi- dimensional MS (MS n where n indicates the number of stages). Glick

m/z: See mass to charge ratio 

: A newer adaptation of ESI methodology in conjunction with MS/MS. Pioneered by Matthias Mann while at EMBL. Only a very small amount of the unseparated peptide mixture is sprayed directly into the MS machine. Many consider this the most sensitive current technique. Can be used with minimal protein sequence (EST) information, but can only be used with purified proteins. Can be used for de novo protein sequencing and study of post-translational modifications.  Alternatively "nanospray MS/MS". Broader term: electrospray

neutral: To the mass spectrometrist, neutral means uncharged, whereas to the biochemist, neutral means underivatized.  Bill Boggess, Review of Mass Spectrometry Desk Reference by O. David Sparkman, 2000  Mass Spectrometry Desk Reference (Sparkman, O. David) Bill Boggess  Journal of Chemical Education 2001 78 (2), 168  DOI: 10.1021/ed078p168.2

Peptide Mass Fingerprinting: Protein technologies  Uses mass spec to identify proteins.

pyrolysis mass spectrometry PyMS:  Wikipedia 

quadrupole ion trap:
A quadrupole ion trap is an instrument roughly the size of a tennis ball whose size is inversely proportional to its versatility. Three hyperbolic electrodes, consisting of a ring and two end caps, form the core of this instruments. In the early 1950’s, Wolfgang Paul and co- workers invented … the quadrupole mass filter … [and] the quadrupole ion trap … The chemistry community’s interest in the trap was confined to several research groups until 1983 when George Stafford and co- workers at Finnigan MAT made two major advances. First they developed the mass-selective instability mode of operation ..and [then] greatly improved the mass resolution. K Jonscher and JR Yates III 
The Quadrupole Ion Trap Mass Spectrometer — A Small Solution to a Big Challenge  ANALYTICAL BIOCHEMISTRY 244, 1–15 (1997)

quadrupole mass analyzer: Arrangements in which ions with a desired quotient mass/ charge are made to describe a stable path under the effect of a static and a high- frequency electric quadrupole field, and are then detected. Ions with a different mass/ charge are separated from the detected ions because of their unstable paths. IUPAC Mass Spectrometry, IUPAC Compendium.

SEQUEST:  Tandem mass spec software program

Secondary Ion Mass Spectrometry SIMS: A mass-spectrometric technique that is used for microscopic chemical analysis. A beam of primary ions with an energy of 5-20 kiloelectronvolts (keV) bombards a small spot on the surface of the sample under ultra-high vacuum conditions. Positive and negative secondary ions sputtered from the surface are analyzed in a mass spectrometer in regards to their mass-to-charge ratio. Digital imaging can be generated from the secondary ion beams and their intensity can be measured. Ionic images can be correlated with images from light or other microscopy providing useful tools in the study of molecular and drug actions.  MeSH, 1995

Selected Reaction Monitoring SRM: SRM 'assays' are generated by defining a signature set of peptide fragment coordinates. A detectable precursor ion–product ion pair is referred to as a 'transition', and several suitable transitions constitute an SRM assay for detection and quantification of a target peptide and, by extension, the target protein. By spiking the sample with heavy isotope–labeled reference peptides, it is possible to achieve absolute quantification of the targeted peptides. The SRM technique is best suited for analyzing about 50–100 proteins concurrently.  Also known as  multiple reaction monitoring (MRM).  Allison Doerr, Mass Spectrometry based targeted proteomics, Nature Methods  10, 23 (2013) doi:10.1038/nmeth.2286 Published online 27 Dec 2012 journal/v10/n1/full/nmeth. 2286.html   Related term: Proteomics targeted proteomics

sequential m/z separation:  45 articles in the MS Terms Wiki, 2005 

soft ionization techniques: Include MALDI and ESI

tandem mass spectrometer MS/MS: An arrangement in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass- charge. A hybrid mass spectrometer is an instrument which combines analysers of different types, e.g. magnetic plus electric sector combined with quadrupole. The study of ions involving two stages of mass analysis has been termed mass spectrometry/ mass spectrometry. IUPAC Mass Spectrometry, IUPAC Compendium

A mass spectrometry technique using two (MS/MS) or more mass analyzers. With two in tandem, the precursor ions are mass-selected by a first mass analyzer, and focused into a collision region where they are then fragmented into product ions which are then characterized by a second mass analyzer. A variety of techniques are used to separate the compounds, ionize them, and introduce them to the first mass analyzer. For example, for in GC-MS/MS, GAS CHROMATOGRAPHY-MASS SPECTROMETRY is involved in separating relatively small compounds by GAS CHROMATOGRAPHY prior to injecting them into an ionization chamber for the mass selection. MeSH 2007

TOF Time-Of-Flight mass spectrometer: An arrangement using the fact that ions of different mass- charge need different times to travel through a certain distance in a field- free region after they have all been initially given the same translational energy. IUPAC Mass Spectrometry, IUPAC Compendium Narrower term: ESI- TOF, MALDI- TOF

top-down mass spectrometry:  In contrast to bottom-up mass spectrometry (MS), top-down approaches involve transferring an undigested protein to the gas phase before dissociation. This allows the mass of an intact protein to be used to identify all splicing and post-translational modification, with each assignable to disparate regions on the polypeptide chain from their corresponding fragment mass values. Until, now however, the tight three-dimensional folding of large molecules when ionized and transferred into the gas phase prevented sufficient fragmentation, restricting application of the approach to proteins <50kDa.  Now McLafferty and colleagues optimize the MS protocol, by modifications  ... to enable fragmentation of proteins four times as large (>2,000 amino acids). Peter Hare, Research Highlights, Top-down mass spectrometry, Nature Biotechnology, 24(11):1367, Nov 2006

triple quadrupole: One of the most popular types of tandem MS instrument is the triple quadrupole mass spectrometer, invented at Michigan State University by In contrast to bottom-up mass spectrometry (MS) Richard A. Yost (now a chemistry professor at the University of Florida, Gainesville) and chemistry professor Christie G. Enke (now at the University of New Mexico, Albuquerque). James D. Morrison of Latrobe University, Melbourne, Australia, helped Yost and Enke reduce the technique to practice. S Borman, "A brief history of mass spectrometry instrumentation" May 1998]

Mass spec resources
Clark, Jim, Understanding Chemistry: Mass Spectrometry Menu
IUPAC International Union of Pure and Applied Chemistry,
Definitions of terms relating to mass spectrometry, 2013     
Mass Spectrometry Terms and Definitions Project Page,  Wiki now contains links to numerous mass spectrometry terminology definitions from the IUPAC Gold Book, Orange Book, 2013 Recommendations, and other sources

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

How to look for other unfamiliar  terms

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