Increasing the Overall Proteome Coverage by Combining Protein Digestion by Tryp-N and Trypsin

Mass spectrometry-based proteomics combining more than one protease in parallel facilitates the identification of more peptides and proteins than when a single protease is used. Trypsin cleaves proteins C-terminally to arginine and lysine, while its mirroring protease Tryp-N cleaves N-terminally to the same amino acids. Here, we combine trypsin and Tryp-N with the commercially available S-Trap columns, which purify protein samples and catalyze digestion. Comparison of trypsin or Tryp-N coupled with S-Trap columns demonstrates plasma and cell lysate proteins unique to one protease. We thus suggest the use of both proteases in a complementary manner to obtain deeper proteome coverage.