Clinical laboratories use electrospray ionization and mass spectrometry (MS)1 every day to measure dozens of different small molecule analytes. The capacity to precisely quantify these biomarkers has improved patient care. To build on the successful implementation of novel MS methodologies, many clinical mass spectrometrists hope to expand the list of measurable analytes to include peptides and proteins, several examples of which have been reported and reviewed (1). One can also envision the translation of novel biomarkers from the research-grade MS assays, with which they are discovered, to clinically acceptable MS assays for diagnosis, prognosis, and evaluation of therapeutic efficacy. An argument can be made that investigators should use clinically acceptable MS assays from the outset (2), which would facilitate the transition from research/discovery to clinical practice. Given the successes over the last few years in precisely measuring proteins by MS in clinically relevant matrices, this outcome may not be too much to ask.
Traditionally, the word proteomics has encompassed efforts aimed at simultaneously measuring many proteins in a given complex sample. Shotgun proteomic experiments, which attempt to identify all of the proteins in a complex sample, and targeted proteomic experiments, which attempt to quantify a subset of the proteins known to exist in a complex sample, can both be carried out using liquid chromatography–tandem MS (LC-MS/MS). Shotgun proteomics is already being used clinically to identify the proteinaceous component of amyloid deposits (3). For the quantification of multiple protein concentrations in a complex sample, however, targeted methods are more precise because data-dependent shotgun proteomic methods variably sample fewer ions across chromatographic peaks. For this reason, targeted approaches are much more likely to be employed in the quantification of proteins in clinical specimens.
Targeted methods typically use proteolysis with trypsin to digest proteins into peptides, which are more amenable to analysis …
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