Recent advances in global-scale proteomic technology enable identification of hundreds of candidate biomarkers. However, very few candidates so identified can reach the high bar of FDA approval for clinical use. The low efficiency of biomarker approval reflects the challenges of taking candidate biomarkers identified in discovery research through the long and difficult pipeline required for biomarker development. The greatest challenge in biomarker development is the lack of reliable assays for use in the verification and validation phases. This paper reviews methodologies and challenges for biomarker assay development with emphasis on stable isotope dilution coupled with multiple reaction monitoring-mass spectrometry (SID-MRM-MS). Because of its sensitivity, quantification abilities, and specificity, SIDMRM- MS has the potential to bridge the critical rate-limiting gaps between the biomarker discovery- and validation phases. A workflow for generation of a specific SID-MRM-MS assay is presented. We conclude that currently, SIDMRM- MS assay is a promising technology for biomarker verification and validation. To move the technology toward an FDA-approvable platform, more stringent evaluation must be performed and these future studies will require a joint effort of the clinical proteomics community, the regulatory agency and major mass spectrometer manufacturers.
Keywords: Mass spectrometry, proteomics, multiple reaction monitoring, biomarker verification, assay development, stable isotope dilution, Chronic obstructive pulmonary disease, Coefficient of variation, Enzyme-linked immunosorbent assay, Tandem mass spectrometry, Concatemer of isotope-labeled marker peptides, Stable isotope labeled internal standard, Stable isotope standards and capture by anti-peptide antibodies