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Tandem mass spectrometers are capable of multiple rounds of mass spectrometry, usually three, with one mass spectrometer used for some form of molecular fragmentation. In molecular applications the first mass spectrometer selects “parent” ions which are passed to the second mass spectrometer which keeps them focused while they are dissociated by collisions with an inert gas or other fragmentation technique. Ion fragments from these collisions, or “daughter” ions, are separated and measured by the third mass spectrometer. MS/MS analytical methods typically call for monitoring ion transitions rather than single ions. This allows for extremely specific and selective identification but cannot be used for the identification of unknowns. In atomic mass spectrometry, the principle is the same except the collisionally induced dissociation in the second chamber is used to remove molecular interferences from the analyte mass of interest. Tandem mass spectrometry can also be performed over time in a single mass spectrometer, such as a quadrupole ion trap, but this approach is currently limited to molecular mass spectrometry applications.

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