Targeted proteomics, specifically “MRM”, can identify and measure the abundance of nearly any protein from any biological sample.  Further, it can measure up to 100 proteins in a single experiment,with high precision and in a reproducible manner (tracking the changes in target proteins across samples and time). Targeted proteomics relies on understanding the signature characteristics of proteins to achieve measurements.

By focusing on a predetermined set of proteins – the ones of most interest - entire pathways or families of molecules can be measured at once.  This allows for deeper, more scientifically useful insight into mode of action studies, biomarker identification, gene expression effects, etc.  More technically, the mass spectrometer can be seen as a two-stage filter in such an experimental set-up. A signal is only generated if the peptide mass and a fragment mass of this peptide matches the current machine programming, or assay. Therefore, a mass spectrometer operating in multiple-reaction monitoring directly acquires elution profiles and not spectra, which can be used to quantify the abundance of the target peptide.

Both survey (shotgun) and targeted (MRM) mass spectrometry proteomics rely on the separation of peptide mixtures by liquid-chromatography. Peptides are separated on a column packed with a sorbent based on a chemical property (e.g. hydrophobicity) and are directly analyzed by a mass spectrometer. The difference between survey and targeted proteomics relies in the type of mass spectrometer, it’s operation, and therefore the range and quality of the data generated.