Diagnostic biomarkers have the potential to impact cancer mortality through early detection, monitoring response to therapy, and monitoring disease recurrence. Discovering biomarker candidates is laborious, requires extensive analysis of a relatively small number of samples, and has a correspondingly high false discovery rate. Validating biomarkers for clinical use requires sensitive and accurate quantification of candidate biomarker proteins in hundreds to thousands of individual samples. In this study we demonstrate the effectiveness of a multi-level mass spectrometry-based platform for discovery and validation of biomarkers, with emphasis on quantification of biomarker candidates. Biomarker candidates are discovered by differential analysis in tumor tissues where the candidates may be more abundant, and then tested in the bloodstream.
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