Mass Spectrometry in Biomarker Applications: From Untargeted Discovery to Targeted Verification, and Implications for Platform Convergence and Clinical Application

It has really been only in the last 10 years that mass spectrometry (MS)2 has had a truly important (but still small) impact on biomedical research. Much of this impact can be attributed to proteomics and its more basic applications. Early biomedical applications have included a number of efforts aimed at developing new biomarkers; however, the success of these endeavors to date have been quite modest—essentially having been confined to preclinical applications—and have often suffered from combinations of immature technology and hubris. Now that MS-based proteomics is reaching adolescence, it is appropriate to ask if and when biomarker-related applications will extend to the clinical realm and what developments will be essential for this transition.Biomarker development can be described as a multistage process consisting of discovery, qualification, verification, research assay optimization, validation, and commercialization (1). From a MS perspective, it is possible to “bin” measurements into 1 of 2 categories—those aimed at discovering potential protein biomarkers and those seeking to verify and validate biomarkers. Approaches in both categories generally involve digesting proteins (e.g., with trypsin) as a first step to yield peptides that can be effectively detected and identified with MS. Discovery-based approaches use broad “unbiased” or “undirected” measurements that attempt to cover as many proteins as possible in the hope of revealing promising biomarker candidates. A key challenge with this approach stems from the extremely large dynamic range (i.e., relative stoichiometry) of proteins of potential interest in biofluids such as plasma and the expectation that biomarker proteins of the greatest clinical value for many diseases may very well be present at low relative abundances (2). Protein concentrations in plasma extend from approximately 1010 pg/mL for albumin to approximately 10 pg/mL and below for interleukins and other cytokines. Proteins secreted or leaking into the blood from specific early-stage …