pepgrep: A Tool for Peptide MS/MS Pattern Matching

of post-translational modifications (PTMs) into the algorithm. Decoy peptide sequences are used or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences useful for examining a CID of small fractions of peptides resulting from, for example, affinity puri-fication techniques. The peptide sequences in such samples are less likely to be positively identified came the front-line method in peptide analysis that is widely leading position among other MS-conducted peptide-sequenc-sequence tag, which, in turn, leads to confident identification of peptide sequences [5,6]. Mascot [7], SEQUEST [8] and TANDEM [9] became the popular software for protein identi-fication based on MS2-to-Peptide and Peptide-to-Protein scor-ing algorithms. Protein database search (PDS) method relies entirely on a premise that the computed theoretical data matches to scanned ion mass spectrum and, in reality, this works only for a relatively small (5–25%) portion of the spec-tra acquired during a single LC–MS run. The biggest ‘silent’ * Corresponding author