---
title: "Mass spectrometry"
chunk: 5/8
source: "https://en.wikipedia.org/wiki/Mass_spectrometry"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T03:41:40.120732+00:00"
instance: "kb-cron"
---

A tandem mass spectrometer is one capable of multiple rounds of mass spectrometry, usually separated by some form of molecule fragmentation. For example, one mass analyzer can isolate one peptide from many entering a mass spectrometer. A collision cell then stabilizes the peptide ions while they collide with a gas, causing them to fragment by collision-induced dissociation (CID). A further mass analyzer then sorts the fragments produced from the peptides. Tandem MS can also be done in a single mass analyzer over time, as in a quadrupole ion trap. There are various methods for fragmenting molecules for tandem MS, including collision-induced dissociation (CID), electron capture dissociation (ECD), electron transfer dissociation (ETD), infrared multiphoton dissociation (IRMPD), blackbody infrared radiative dissociation (BIRD), electron-detachment dissociation (EDD) and surface-induced dissociation (SID). An important application using tandem mass spectrometry is in protein identification.
Tandem mass spectrometry enables a variety of experimental sequences. Many commercial mass spectrometers are designed to expedite the execution of such routine sequences as selected reaction monitoring (SRM), precursor ion scanning, product ion scanning, and neutral loss scanning.

In SRM, the first analyzer allows only a single mass through and the second analyzer monitors for multiple user-defined fragment ions over longer dwell-times than could be achieved in a full scan. This increases sensitivity.
In product ion scans, the first mass analyzer is fixed to select a particular precursor ion ("parent"), while the second is scanned to find all the fragments ("products", or "daughter ions") to which it can be fragmented in the collision cell.
In precursor ion scans, the second mass analyzer is fixed to select a particular fragment ion ("daughter"), while the first is scanned to find all possible precursor ions that could give rise to this fragment.
In neutral loss scans, the two mass analyzers are scanned in parallel, but separated by the mass of a molecular subunit of interest to the analyst. Ions are detected if they lose that fixed mass during fragmentation. This can be used to look for any chemical that is capable of losing a particular neutral group, for example a sugar residue. Together, neutral loss and precursor ion scans can be used to hunt for chemicals with particular motifs.
Another type of tandem mass spectrometry used for radiocarbon dating is accelerator mass spectrometry (AMS), which uses very high voltages, usually in the mega-volt range, to accelerate negative ions into a type of tandem mass spectrometer.
The METLIN Metabolite and Chemical Entity Database is the largest repository of experimental tandem mass spectrometry data acquired from standards. The tandem mass spectrometry data on over 960,000 molecular standards (as of October 2025) is provided to facilitate the identification of chemical entities from tandem mass spectrometry experiments. In addition to the identification of known molecules it is also useful for identifying unknowns using its similarity searching/analysis. All tandem mass spectrometry data comes from the experimental analysis of standards at multiple collision energies and in both positive and negative ionization modes.

== Common mass spectrometer configurations and techniques ==
When a specific combination of source, analyzer, and detector becomes conventional in practice, a compound acronym may arise to designate it succinctly. One example is MALDI-TOF, which refers to a combination of a matrix-assisted laser desorption/ionization source with a time-of-flight mass analyzer. Other examples include inductively coupled plasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS), thermal ionization-mass spectrometry (TIMS) and spark source mass spectrometry (SSMS).
Certain applications of mass spectrometry have developed monikers that although strictly speaking would seem to refer to a broad application, in practice have come instead to connote a specific or a limited number of instrument configurations. An example of this is isotope-ratio mass spectrometry (IRMS), which refers in practice to the use of a limited number of sector based mass analyzers; this name is used to refer to both the application and the instrument used for the application.

== Separation techniques combined with mass spectrometry ==
An important enhancement to the mass resolving and mass determining capabilities of mass spectrometry is using it in tandem with chromatographic and other separation techniques.

=== Gas chromatography ===

A common combination is gas chromatography-mass spectrometry (GC/MS or GC-MS). In this technique, a gas chromatograph is used to separate different compounds. This stream of separated compounds is fed online into the ion source, a metallic filament to which voltage is applied. This filament emits electrons which ionize the compounds. The ions can then further fragment, yielding predictable patterns. Intact ions and fragments pass into the mass spectrometer's analyzer and are eventually detected. However, the high temperatures (300 °C) used in the GC-MS injection port (and oven) can result in thermal degradation of injected molecules, thus resulting in the measurement of degradation products instead of the actual molecule(s) of interest.

=== Liquid chromatography ===

Similarly to gas chromatography MS (GC-MS), liquid chromatography-mass spectrometry (LC/MS or LC-MS) separates compounds chromatographically before they are introduced to the ion source and mass spectrometer. It differs from GC-MS in that the mobile phase is liquid, usually a mixture of water and organic solvents, instead of gas. Most commonly, an electrospray ionization source is used in LC-MS. Other popular and commercially available LC-MS ion sources are atmospheric pressure chemical ionization and atmospheric pressure photoionization. There are also some newly developed ionization techniques like laser spray.

=== Capillary electrophoresis–mass spectrometry ===

Capillary electrophoresis–mass spectrometry (CE-MS) is a technique that combines the liquid separation process of capillary electrophoresis with mass spectrometry. CE-MS is typically coupled to electrospray ionization.

=== Ion mobility ===