Mass spectrometry functions

Mass spectrometry has four essential functions, which are ionization, separation (filtering), detection and analysis. These functions are coordinated by the following components: the ion source, mass analyzer, detector and software. When combined with chromatography, such as liquid or gas chromatography, the potential for MS to identify and quantitate analytes of interest increases dramatically.

Atoms and molecules must first be ionized before they can be accelerated through the mass spectrometer and detected. This is because mass spectrometers separate particles by calculating their different mass-to-charge ratios (m/z). Example ionization methods include atmospheric pressure chemical ionization (APCI), electron ionization (EI), electrospray ionization (ESI), chemical ionization (CI) inductively coupled plasma (ICP) ionization and matrix-assisted laser desorption/ionization (MALDI).

The analyzer separates and stores charged ions based on their polarities. Some examples of mass analyzers include quadrupoles, triple quadrupoles, ion traps, Orbitraps, Fourier transform, magnetic sectors and time-of-flight (TOF) instruments. Different analyzers excel at different functions; for example, quadrupoles are often used in quantitative studies, while ion traps are chosen for qualitative and structural work. Different analyzers are also combined in hybrid and tribrid mass spectrometers.

Charged ions can be detected with electron multipliers, scintillators or Faraday cups. In each case, the detectors multiply the signal produced by the incident ion using dynodes or photon multipliers.

Mass spectrometry is an analysis method that can be performed once using a single analyzer, or it can be performed in tandem between different mass analyzers (such as those found in hybrid or tribrid mass spectrometers). The practice of simultaneous MS is frequently termed tandem mass spectrometry (MS/MS or MS2) and refers to two or more reaction steps being performed on selected ions. In the first step of mass analysis, precursor ions are formed in the ion source and induced to fragment. In the second step, the fragmentation products are detected and analyzed. Selection of both precursor and fragment ions, as well as their number during each step of the process, can vary depending on the goal of the analysis.

In this section, you will understand the following:

  • The different options for sample ionization using ion sources.
  • The differences between commonly used mass analyzers.
  • The general operation of mass spectrometers, including hybrid and tribrid mass spectrometers.
  • The different approaches to sample labeling and mass spectrometry analysis.

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Mass spectrometry technology subtopics

Mass Analyzer Technology Overview

The heart of the mass spectrometer is its mass analyzer. Learn more about how mass analyzers separate, select and even fragment ions based on their distinct masses and charges.

Ionization Source Technology Overview

Samples must be ionized (or charged) before they can be manipulated by electric and magnetic fields within the mass spectrometer. Click here to understand the different methods used to make samples cationic or anionic depending on their inherent properties and the ionzation source.

Dissociation Technique Technology Overview

Follow the process molecular fragmentation, used in fields such as proteomics, which is required for the identification and quantitation of primary sequences and post-translational modifications.


Wilm, M (2011) Principles of electrospray ionization. Mol & Cell Proteomics 10(7):1-8. PMC

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