DETAILED PEPTIDE CHARACTERIZATION USING PEPTIDEMASS - A WORLD-WIDE-WEB-ACCESSIBLE TOOL

In peptide mass fingerprinting, there are frequently peptides whose ma sses cannot be explained. These are usually attributed to either a mis sed cleavage site during the chemical or enzymatic cutting process, th e lack of reduction and alkylation of a protein, protein modifications like the oxidation of methionine, or the presence of protein post-tra nslational modifications. However, they could equally be due to databa se errors, unusual splicing events, variants of a protein in a populat ion, or artifactual protein modifications. Unfortunately the verificat ion 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 ''PEPTI DE-MASS''. This program generates the theoretical peptide masses of an y 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 th e predicted masses of peptides from proteins which are known to have s ignal sequences, propeptides, transit peptides, simple post-translatio nal modifications, and disulfide bonds. Users are also warned if any p eptide masses are subject to change from protein isoforms, database co nflicts, or an mRNA splicing variation. The program is freely accessib le to the scientific community via the ExPASy World Wide Web server, a t the URL address: http://www.expasy.ch/www/tools.html.