Detailed peptide characterization using PEPTIDEMASS – a World‐Wide‐Web‐accessible tool

Abstract

In peptide mass fingerprinting, there are frequently peptides whose masses cannot be explained. These are usually attributed to either a missed cleavage site during the chemical or enzymatic cutting process, the lack of reduction and alkylation of a protein, protein modifications like the oxidation of methionine, or the presence of protein post-translational modifications. However, they could equally be due to database errors, unusual splicing events, variants of a protein in a population, or artifactual protein modifications. Unfortunately the verification of each of these possibilities can be tedious and time-consuming. To better utilize annotated protein databases for the understanding of peptide mass fingerprinting data, we have written the program "PEPTIDEMASS". This program generates the theoretical peptide masses of any protein in the SWISS-PROT database, or of any sequence specified by the user. If the sequence is derived from the SWISS-PROT database, the program takes into account any annotations for that protein in order to generate the peptide masses. In this manner, the user can obtain the predicted masses of peptides from proteins which are known to have signal sequences, propeptides, transit peptides, simple post-translational modifications, and disulfide bonds. Users are also warned if any peptide masses are subject to change from protein isoforms, database conflicts, or an mRNA splicing variation. The program is freely accessible to the scientific community via the ExPASy World Wide Web server, at the URL address: http://www.expasy.ch/www/tools.html.