Since Nielsen et al. (J Proteome Res 2002, 1, 63) reported the usefulness of peptide “end sequencing” using MALDI Q-TOFMS, product ion information generated by tandem mass spectrometry from both peptide termini have been widely used to facilitate protein identification. For example, the N-terminal amino acid determined by the presence of a1 and/or b1 ions can reduce the search space in database search to 1/19. Likewise, y1 ion can determine the C-terminal amino acid, reducing the search space down to 1/2 for tryptic peptides. Here, we investigated the utility of product ions from the peptide end sequence, obtained by LC/ESI/Q-orbitrap instruments with HCD fragmentation.
One data file from a public dataset (PXD005159) was used as a sample dataset, and 44,047 spectra were searched by Mascot against Swiss-Prot human all sequence database. The annotated peak list was obtained and the peptide end sequence information as well as immonium (iminium) ions were investigated.
Out of the 26,321 total annotated spectra, immonium ions, a2 ions, y1 ions and y2 ions were observed in 17,894, 18,661, 10,134 and 20,059 spectra, respectively; y1 ions were observed in 86% of all spectra. These tendencies were the same as those observed by Nielsen et al.
HCD spectra by LC/ESI/Q-orbitrap contain rich information on peptide end sequence, which can be utilized to facilitate peptide/protein identification. In this poster, the results for the large-scale datasets will be described.