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Tandem mass spectrometry (MS/MS, also written tandem MS) is a mass spectrometry technique in which ions of one chosen mass-to-charge ratio are isolated, fragmented, and then measured again. This guide explains how that works, compares the main scan modes, and sets out what a clinical or research lab should weigh when using it. It is general technical information, not instrument-specific or medical advice.
Short answer: what is MS/MS spectrometry?
MS/MS uses two rounds of mass analysis. Ions are first selected by mass-to-charge ratio (m/z), then fragmented, and the fragments are separated by m/z in a second round. Thermo Fisher describes it this way: “Tandem mass spectrometry (MS/MS) offers additional information about specific ions.” Because an analyte is recognised by its precursor mass and by its fragments, identification and quantitation are more selective than with a single mass measurement.
Definition and scope
“MS/MS”, “tandem MS” and “tandem mass spectrometry” are synonyms in common use. The technique is applied in two broad ways: to identify unknown molecules (for example, sequencing peptides) and to quantify known ones with high selectivity. For a general introduction to the instrument itself, see what a mass spectrometer is.
How MS/MS works: select, fragment, analyse
1. Select the precursor ion
On a triple quadrupole instrument, the first mass-analysing quadrupole (Q1) is set to transmit a narrow mass window around the desired parent (precursor) ion (Yocum and Chinnaiyan, 2009).
2. Fragment it
In the same instrument, fragmentation by collision-induced dissociation (CID) occurs in the second quadrupole (Q2). More generally, Thermo Fisher lists collision with an inert gas (CID or higher-energy collision dissociation, HCD) and electron-based approaches (electron-transfer dissociation, ETD, and electron-capture dissociation, ECD) as ways to fragment selected ions.
3. Analyse the fragments
The third quadrupole (Q3) acts as the second mass-analysing filter, passing a chosen fragment ion to the detector. For identification work, the fragment pattern can be matched to predicted peptide or nucleic acid sequences in databases such as IPI, RefSeq and UniProtKB/Swiss-Prot. The protein sequencing by mass spectrometry guide and the fragmentation rules guide go further on this.
MS/MS scan modes compared
The same hardware can be run in different ways depending on the question asked. Each row below is limited to what the cited review states.
| Mode | What the instrument does | Question it answers |
|---|---|---|
| Full-scan MS/MS (product ion spectrum) | A full scan MS/MS spectrum is gathered, for example on a linear ion trap or TOF/TOF instrument | What fragments does this precursor give? Used to characterise peptides at the discovery stage |
| Selected reaction monitoring (SRM) | Q1 passes one precursor, Q3 passes one fragment; the pair is one transition | Is this specific analyte present, and how much? A positive result requires two ions |
| Multiple reaction monitoring (MRM) | Several transitions are monitored within one run | Several targets at once, at a cost in dwell time per transition |
| Inclusion list scanning | Precursor masses of interest are listed for detection rather than scanning the entire mass range | Are these pre-chosen precursors present? |
| Neutral loss (NL) | Looks for loss of a characteristic fragment, such as the phosphate group from phosphopeptides | Which precursors carry that modification? |
| Product ion monitoring (PIM) | Monitors the product ion after CID rather than the precursor, in a SIM-like approach | Is this fragment present after fragmentation? |
Source for the table: Yocum and Chinnaiyan (2009). The review notes that triple quadrupole instruments are the main platform for SRM and MRM, and that dwell time and cycle time are directly proportional and affect sensitivity: longer dwell time improves sensitivity but lengthens the cycle, so fewer transitions can be measured. Practical tuning is covered in MRM transitions, dwell time and cycle time, and the SRM concept in selected reaction monitoring.
Where MS/MS matters in labs
In clinical laboratories, MS/MS is usually coupled to liquid chromatography (LC-MS/MS); see LC-MS explained and the ionisation step in electrospray ionisation. Jannetto (Clinical Laboratory News, ADLM, 2015) gives the points below, which form a checklist when weighing MS/MS against an immunoassay:
- Specificity. Immunoassays suffer from limitations including problems with specificity; MS/MS has superior selectivity for many analytes because it recognises them by at least two physical properties.
- Retention time. With LC in front, retention time adds another property to identify the analyte correctly.
- Method development. Choosing suitable internal standards is among the challenges of method development, and validation of laboratory-developed tests must address issues such as ion suppression.
- Standardisation. LC-MS/MS assays are not standardised or harmonised, and commercial calibrators are not available, so results can differ between laboratories.
Common misunderstandings
- MS/MS is not two separate instruments. On a triple quadrupole the two analysis rounds happen in sequence within one instrument, with Q2 serving as the fragmentation region.
- SRM and MRM are not different physics. MRM is SRM with several transitions monitored in one run.
- Higher selectivity does not mean no interference. Ion suppression and method-validation issues remain, as the ADLM article notes.
Frequently asked questions
What is the principle of MS/MS spectrometry?
Select an ion by m/z, fragment it (for example by collision with an inert gas), then separate and detect the fragments by m/z.
What are the applications of MS/MS?
The sources above describe sequencing proteins and oligonucleotides by database matching, targeted quantitation of peptides by SRM/MRM, and clinical LC-MS/MS testing.
Is tandem MS the same as MS/MS?
Yes. Tandem MS, tandem mass spectrometry and MS/MS name the same approach. See also how to read a mass spectrum.
Sources
- Yocum AK, Chinnaiyan AM. Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. Brief Funct Genomic Proteomic 2009;8(2):145-157. pmc.ncbi.nlm.nih.gov/articles/PMC2722263 (read 2026-11-08).
- Thermo Fisher Scientific. Overview of Mass Spectrometry for Protein Analysis. thermofisher.com (read 2026-11-08).
- Jannetto P. Liquid Chromatography Tandem Mass Spectrometry: The Swiss Army Knife for Clinical Laboratories. Clinical Laboratory News, ADLM, 1 July 2015. myadlm.org (read 2026-11-08).
