Proteomic Analysis of Human Blood Serum Using Peptide Library Beads

Human serum is thought to contain key information for diagnostics of human disease. However, no
single technology is currently nor might ever be available to cope with the complexity and dynamic
range of the serum proteome. We here report a large-scale proteomic study of human blood serum
using peptide library beads and mass spectrometry. Serum proteins are adsorbed onto polymeric beads
coated with a combinatorial library composed of millions of hexameric peptide baits. Analysis of the
eluates from this combinatorial library (as obtained with 3 eluants of different strength, able to release
99% of the retentate) via liquid chromatography coupled to high-resolution mass spectrometry resulted
in the identification of 1559 proteins or 3869 proteins, respectively, depending on how 95% confidence
was estimated. In either case, the analysis showed that ligand beads are able to capture a large number
of proteins in a single operation. The ligand bead bound fraction appeared to have a lower dynamic
range when compared to the starting material, due to a “normalization” of the protein concentrations
in the original mixture. We find that extensive information on the protein composition of complex
samples such as serum can be obtained using ligand beads and that these beads enrich the proteomic
tool box.
Keywords: serum proteins • ligand library • peptide ligands