Multiple parameter cross-species protein identification using MultiIdent -a World-Wide Web accessible tool

Recent increases in the number of genome sequencing projects means that the amount of protein sequence in databases is increasing at an astonishing pa ce. In proteome studies, this is facilitating the identification of protein s from molecularly well-defined organisms. However, in studies of proteins from the majority of organisms, proteins must be identified by comparing an alytical data to sequences in databases from other species. This process is known as cross-species protein identification. Here we present a new progr am, MultiIdent, which uses multiple protein parameters such as amino acid c omposition, peptide masses, sequence tags, estimated protein pI and mass, t o achieve cross-species protein identification. The program is structured s o that protein amino acid composition, which is highly conserved across spe cies boundaries, first generates a set of candidate proteins. These protein s are then queried with other protein parameters such as sequence tags and peptide masses. A final list of database entries which considers all analyt ical parameters is presented, ranked by an integrated score. We illustrate the power of the approach with the identification of a set of standard prot eins, and the identification of proteins from dog heart separated by two-di mensional gel electrophoresis. The MultiIdent program is available on the w orld-wide web at: http://www.expasy.ch/sprot/multiident.html.