Tandem mass spectrometry (MS/MS) involves two or more stages of mass analysis, enabling the selection of a precursor ion and the analysis of its fragment ions. This provides detailed structural information and enables highly specific quantification in complex matrices.

MS/MS experiments follow the sequence of precursor ion selection, fragmentation, and mass analysis of the fragment ions. Precursor ions of a selected m/z value are isolated in the first mass analyzer. Fragmentation is induced by collision-induced dissociation with inert gas molecules, electron capture/transfer dissociation, or photon activation. The resulting fragment ions are analyzed in the second mass analyzer.

Tandem-in-space instruments separate the mass analysis stages in different physical regions. Triple quadrupole (QqQ) instruments use two quadrupole mass filters separated by a collision cell and are the workhorses of quantitative LC-MS/MS. Quadrupole time-of-flight (Q-TOF) instruments combine a quadrupole for precursor selection with a high-resolution TOF analyzer. Tandem-in-time instruments perform multiple stages in the same physical space, as in ion trap instruments.

Common scan modes include product ion scanning, where the precursor is fixed and fragments are scanned; precursor ion scanning, where the fragment is fixed and precursors are scanned; and neutral loss scanning, where both analyzers scan with a fixed mass offset. Multiple reaction monitoring (MRM) fixes both precursor and fragment for maximum sensitivity and specificity in quantification.

MS/MS is essential for proteomics, metabolomics, forensic toxicology, clinical diagnostics, and environmental analysis. Its ability to resolve isobaric compounds and provide structural confirmation makes it the gold standard for quantitative bioanalysis.