Blood is a convenient source of biomarkers. Readily obtainable, it immerses most tissues in the body and is therefore likely to contain cell-derived proteins and peptides that may provide information about various biological processes. Serum proteome and peptidome profiling--using mass spectrometry (MS), for example--may thus show a functional correlate of biological events and disorders. To this end, serum peptides must be enriched and interfering substances removed: a step that should be automated to a degree, reproducible and free of bias if it is to generate a test with any future diagnostic potential. The current protocol allows simultaneous analysis of large numbers of peptides using reversed-phase, magnetic particle-assisted sample processing with a matrix-assisted laser desorption/ionization-time of flight MS readout. It may be used for diagnostic or predictive purposes, specifically as an in vitro readout of proteolytic activities with qualitative and quantitative product analysis, and enables profiling of 96 samples in less than 27 h.