From Lost in Translation to Paradise Found: Enabling Protein Biomarker Method Transfer by Mass Spectrometry

Recently, Begley and Ellis delivered a sobering message to laboratories around the world (1). The lack of meaningful progress in preclinical cancer research was highlighted by the irreproducibility of >70% of published studies. The authors also crystallized the importance of full disclosure and the validation of critical scientific discoveries for industry-wide improvement. Translation of novel biomarkers into clinical care for the evaluation of therapeutic safety and efficacy has been slow (2), partly because of the cost and complexity of immunoassay development. The potential for liquid chromatography–tandem mass spectrometry (LC-MS/MS)3 to streamline the translation of novel protein biomarkers is profound (3).Most LC-MS/MS-based protein assays incorporate denaturation and proteolytic digestion of proteins in the sample into peptides (traditionally called “bottom-up” proteomics). These preparative steps destroy potentially interfering proteins into peptides that can be resolved and ignored by LC-MS/MS (4). Inclusion of stable isotope–labeled internal standard proteins or peptides (which may be cleavable) in each sample enables correction for matrix effects, including sample-related digestion variability and/or ion suppression, both significant analytical benefits compared with immunoassays.Downstream members of the scientific community are hopeful about translating important preliminary findings into clinical practice; however, success has been hampered by a lack of transparency and insufficient validation. Consequently, LC-MS/MS-based clinical protein analysis has predominantly focused on improved analytical measurement for well-established biomarkers (5). This is despite “fit-for-purpose” criteria for enablement (6, 7) and published recommendations for analytical validation (8), based primarily on U.S. Food and Drug Administration guidance (9). Although assays used in preclinical research are generally not held to the same standards as assays used in the immediate care of patients, which are governed by CLIA-88 and by extension many Clinical Laboratory Standards Institute consensus documents, published fundamental discovery experiments and biomarker verification studies spawn costly research programs. To advance our …