MALDI-TOF serum profiling using semiautomated serum peptide capture with magnetic reversed phase (C18) beads.

Mass spectrometry can be used to generate diagnostic peptide peak profiles "signatures" of serum samples. Peak profiles can be used to compare different sera and correlate samples (i.e., patient groups) with clinical data to assist in diagnosis, monitoring, and/or prediction. We describe the semiautomated capture of serum peptides/small proteins with magnetic beads that harbor C18 alkyl chains, the deposition of captured material on a target plate for MALDI-TOF mass spectrometry, as well as, general guidelines for data acquisition. We also include, in a separate note, a short manual version of the capture procedure. Overall, the serum sample processing protocol, reported here, is reproducible and robust. In conjunction with MALDI-TOF mass spectrometry, this protocol allows for the profiling of several hundreds of serum peptides.