Enhanced identification of peptides lacking basic residues by LC-ESI-MS/MS analysis of singly charged peptides
16.05.2012
Biniossek ML, Schilling O
Proteomics. 2012 May;12(9):1303-9
Pepptide sequences lacking basic residues (arginine, lysine, or histidine, referred to as “base-less”) are of particular importance in proteomic experiments targeting protein C-termini or employing non–tryptic proteases such as GluC or
chymotrypsin. We demonstrate enhanced identification of base–less peptides by focused analysis of singly charged precursors in liquid chromatography (LC) electrospray ionization tandem mass spectrometry (MS/MS). Singly charged
precursors are often excluded from fragmentation and sequence analysis in LC– MS/MS. We generated different pools of base–less and base–containing peptides by tryptic and non-tryptic digestion of bacterial proteomes. Focused LC–MS/MS analysis of singly charged precursor ions yielded predominantly base–less peptide identifications. Similar numbers of base–less peptides were identified by LC–MS/MS analysis targeting multiply charged precursors. There was little redundancy between the base–less sequences derived by both MS/MS schemes. In the present experimental outcome, additional LC–MS/MS analysis of singly charged precursors substantially increased the identification rate of base–less sequences derived from multiply charged precursors. In conclusion, LC–MS/MS based identification of base–less peptides is substantially enhanced by additional focused analysis of singly charged precursors.
