Historically, classical proteomics was based on a global, or ”shotgun”, method, where a mixture of proteins is digested into peptides, fractionated and analyzed by mass spectrometry.  The theory was that analysis including hundreds or thousands of proteins at once would lead to the discovery of all proteins in the sample, though in practice this is extremely challenging, requiring huge resources and delivering more data than any investigator could make useful.

In practice, most experiments do not require a global view. Rather, researchers are most interested about what happens to a relatively small number of proteins under different conditions. 

Targeted proteomics (more specifically multiple reaction monitoring, MRM) offers a solution for these cases. Specialized mass spectrometer (tripple quadrupoles, QQQ) can be programmed to focus on only the targets of interest which in turn provides significant gains in sensitivity and dynamic range.

These programs are called MRM assays. Development of these assays is an extensive process, but once generated for a particular protein, this mass spectrometric assay can be deployed for the accurate identification and quantification of that protein across biological samples.

In MRM, the first and the third quadrupoles act as filters to specifically select predefined m / z values corresponding to the peptide ion and a specific fragment ion of the peptide, whereas the second quadrupole serves as collision cell. Several such transitions (precursor / fragment ion pairs) are monitored over time, yielding a set of chromatographic traces with the retention time and signal intensity for a specific transition as coordinates. The two levels of mass selection with narrow mass windows result in a high selectivity - background ions are filtered out.