There is an urgent need for accurate biomarkers of disease. The low-molecular weight proteome of blood serum or other biological fluids may be an ideal source of such biomarkers, although its analysis requires high-throughput strategies to enrich and quantify peptides and small proteins with biomarker potential. Herein, serum samples from cancer cases and controls are compared using a workflow of robotic reversed-phase extraction and clean-up, followed by automated MALDI MS spectral acquisition and analysis of the low-molecular weight peptidome. The aim of the presented methodology is to facilitate the discovery of candidate serum biomarkers of cancer using MALDI MS profiling, although the method is applicable to any comparative proteomic analysis of any biofluid
