Flexible and fast mapping of peptides to a proteome with ProteoMapper

Luis Mendoza, Eric W. Deutsch, Zhi Sun, David S Campbell, David D. Shteynberg, Robert L. Moritz
2018 Journal of Proteome Research  
Bottom-up proteomics relies on the proteolytic or chemical cleavage of proteins into peptides, the identification of those peptides via mass spectrometry, and the mapping of the identified peptides back to the reference proteome to infer which possible proteins are identified. Reliable mapping of peptides to proteins still poses substantial challenges when considering similar proteins, protein families, splice isoforms, sequence variation, and possible residue mass modifications, combined with
more » ... n imperfect and incomplete understanding of the proteome. The ProteoMapper tool enables a comprehensive and rapid mapping of peptides to a reference proteome. The indexer component creates a segmented index for an input proteome from a FASTA or PEFF file. The ProMaST component provides ultrafast mapping of one or more input peptides against the index. ProteoMapper allows searches that take into account known sequence variation encoded in PEFF files. It also enables fuzzy searches to find highly similar peptides with residue order changes or other isobaric or near-isobaric substitutions within a specified mass tolerance. We demonstrate an example of a one-hit-wonder identification in PeptideAtlas that may be better explained by a combination of catalogued and uncatalogued sequence variation in another highly observed protein. ProteoMapper is a free and open source, available for local use after downloading, embedding in other applications, as an online web tool at http://www.peptideatlas.org/map , and as a web service.
doi:10.1021/acs.jproteome.8b00544 pmid:30230343 pmcid:PMC6438762 fatcat:vleknfus3rcrbot6tf5lzvkr5e