Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry

SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (M S/MS), which was initially developed for the automated interpretation of hi gh-energy collision-induced dissociation (CID) MS/MS spectra of peptides, h as been applied to the interpretation of low-energy CID and post-source dec ay (PSD) spectra of peptides. Based on peptide backbone fragmented ions and their related ions, which are the dominant ions observed in the latter two techniques, the types of ions and their propensities to be observed have b een optimized for efficient interpretation of the spectra. in a typical exa mple, the modified SeqMS allowed the complete sequencing of a 31-amino acid synthetic peptide, except for the isobaric amino acids (Leu or lie, and Ly s or Gin), based on only the low-energy CID-MS/MS spectrum.