Automated Calculation of Unique PeptideSequencesforUnambiguous Identification of HighlyHomologousProteins byMassSpectrometry

Abstract

In regular proteomics approaches proteases are used to digest the proteome into a set of peptides. Unfortunately, determining proteins on the basis of peptides implies some uncertainty since a peptide may be part of different proteins. Therefore, a targeted detection of unique peptides of particular proteins is a promising task for an unambiguous identification of a specific protein. Here we present a software solution that offers the possibility for a highly efficient and simple detection of such unique peptides. In a first step a SQL-based database of theoretically digested peptides from a given FASTA file formatted protein database is generated by choosing a protease. In a second step, in silico generated peptides from a pre-defined protein sequence are compared to this peptide database in order to identify unique peptides. Amongst others, possible applications are identification of proteins when only sparse peptide information is available or advanced proteomics techniques that require information about the uniqueness of peptides such as Multiple Reaction Monitoring (MRM).