How is Tandem Mass Spectrometry Used in the Life Sciences?

In this article, we explore the benefits and applications of using Tandem Mass Spectrometry in the Life Sciences. Continue reading to learn more. 

Scientist woman indicates the chromatogram of mass spectrometry analysis results of compounds, as shown on the computer monitor of mass spectrometer instrument in the laboratory.

Image Credit: S. Singha/

Mass spectrometry is a widely used chemical identification and quantification method in a diverse range of samples. The basic principle of mass spectrometry is that the chemical species in the sample are ionized and undergo some degree of fragmentation.1
By measuring the mass-to-charge ratios of the species produced either by direct ionization or fragmentation, a ‘chemical fingerprint’ can be constructed that contains information on the elemental species present. With the right analysis, fragmentation patterns can also be used to work out local regions of chemical structure as well.

One of the challenges for mass spectrometry applications in the life sciences is that the molecular species tend to have very large masses, complex fragmentation patterns and may also be embedded in chemically complex matrices or sample environments.

Mass spectrometers can only measure finite mass ranges and so one way of dealing with the large molecular weights of many biological macromolecules is to use tandem mass spectrometry.2

Tandem mass spectrometry uses a series of mass spectrometers for sequential sample analysis. In tandem mass spectrometry, the initial biomolecule is ionized and fragmented before a series of particular ions are selected by their mass-to-charge ratio before undergoing further fragmentation and analysis.3

Tandem mass spectrometry in its simplest form is mass spectrometry-mass spectrometry (MS-MS), but there are variations, particularly for the analysis of very large macromolecules that may have even more tandem mass spectrometry stages as part of the instrument for multiple ion selection and fragmentation steps.

Instrumentation and Method

There are many different mechanisms and approaches to ionization that are used in tandem mass spectrometry. ‘Soft’ ionization techniques such as MALDI, which induce little fragmentation in the biomolecule, can be very useful in life sciences for avoiding excessive fragmentation in a single analysis step in tandem mass spectrometry.4 As tandem mass spectrometry uses multiple fragmentation steps as opposed to single mass spectrometry, it is important that the masses selected are sufficiently large that subsequent fragmentation is meaningful.

Depending on the required mass ranges and mass to charge resolution required, there are a number of detection options in tandem mass spectrometry.5 Most detectors are based on time-of-flight, where the charged particles produced from ionization travel through a set distance and how long this takes is proportional to their mass.

Quadrupoles are commonly used in time-of-flight detection systems for tandem mass spectrometry as they allow for the necessary mass selection while still achieving the high mass resolution of time-of-flight systems.6

Key Applications of Tandem Mass Spectrometry

Some of the key applications of tandem mass spectrometry in the life sciences include proteomics, metabolomics and pharmacokinetics.

Proteomics uses tandem mass spectrometry to identify the nature of peptides in protein sequences.7 For this application, the mass selection capabilities of tandem mass spectrometry are very useful as they can be used to generate fragment ion spectra to identify specific peptide ions.

In metabolomics, tandem mass spectrometry is used to identify metabolites in biological tissues.8 One challenge for metabolomics is the complex mixtures of chemical species present, which often means that a combination of hyphenated and tandem mass spectrometry methods need to be used to achieve sufficient species separation before the tandem mass spectrometry can be used for identification.

Pharmacokinetic studies attempt to elucidate what the body does to a drug species when it is metabolized or interacts with tissues. Tandem-mass spectrometry can be used as part of these studies to help identify potential metabolic products and to establish how a drug works.

Tandem Mass Spectrometry in Life Sciences: Case Studies

Possibly one of the most significant impacts of tandem mass spectrometry has been its adoption in clinical settings. One of the impacts tandem mass spectrometry has had on the reduction of false positive rates from above 1 % to less than 0.26 % for screening newborn babies for a series of health disorders.9 Providing an extra dimension of mass information in tandem mass spectrometry can improve confidence in the identification of particular amino acids, which are important clinical screening and diagnostic markers.

While there are challenges associated with the clinical training and competencies in the use of tandem mass spectrometry, the improved quality of clinical assays make it an appealing diagnostic tool.

The same analytical capabilities that make tandem mass spectrometry appealing for metabolomics studies also make tandem mass spectrometry a useful tool in the diagnosis and screening of metabolic diseases that often manifest as issues with the catabolism of specific amino acids.10

Challenges and Conclusion

Meaningful interpretation of spectra is a challenge for many techniques, and for identifying unknown compounds, where there is no existing database data for comparison, can rely on very skilled personnel. The great adoption of automated analysis and unsupervised learning techniques may help to improve throughput for tandem mass spectrometry and encourage further uptake of the technique in clinical settings.

Overall, the compatibility of tandem mass spectrometry with a range of sample types, the richness of the obtained information and the ability to perform selective and controlled studies on specific mass fragments make tandem mass spectrometry a highly useful tool in the life sciences and drug development.


Glish, G. L., & Vachet, R. W. (2003). The basics of mass spectrometry in the twenty-first century. Nature Reviews Drug Discovery, 2(2), 140–150.

Büyükköroğlu, G., Dora, D. D., Özdemir, F., & Hizel, C. (2018). Techniques for protein analysis. In Omics Technologies and Bio-engineering: Towards Improving Quality of Life (Vol. 1).

Pól, J., Strohalm, M., Havlíček, V., & Volný, M. (2010). Molecular mass spectrometry imaging in biomedical and life science research. Histochemistry and Cell Biology, 134(5), 423–443.

Kind, T., & Fiehn, O. (2010). Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev, 2, 23–60.

Medhe, S. (2018). Mass Spectrometry: Detectors Review. Chemical and Biomolecular Engineering, 3(4), 51–58.

Allen, D. R., & McWhinney, B. C. (2019). Quadrupole Time-of-Flight Mass Spectrometry: A Paradigm Shift in Toxicology Screening Applications. Clinical Biochemist Reviews, 40(3), 135–146.

Nesvizhskii, A. I., Vitek, O., & Aebersold, R. (2007). Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods, 4(10), 787–797.

Ceglarek, U., Leichtle, A., Brügel, M., Kortz, L., Brauer, R., Bresler, K., Thiery, J., & Fiedler, G. M. (2009). Challenges and developments in tandem mass spectrometry based clinical metabolomics. Molecular and Cellular Endocrinology, 301(1–2), 266–271.

Mittal, R. D. (2015). Tandem Mass Spectroscopy in Diagnosis and Clinical Research. Indian Journal of Clinical Biochemistry, 30(2), 121–123.

Rashed, M. S. (2001). Clinical applications of tandem mass spectrometry: Ten years of diagnosis and screening for inherited metabolic diseases. Journal of Chromatography B: Biomedical Sciences and Applications, 758(1), 27–48.

Further Reading

Last Updated: Dec 11, 2023

Rebecca Ingle, Ph.D

Written by

Rebecca Ingle, Ph.D

Dr. Rebecca Ingle is a researcher in the field of ultrafast spectroscopy, where she specializes in using X-ray and optical spectroscopies to track precisely what happens during light-triggered chemical reactions.


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