The complete peptide dictionary--a meta-proteomics resource

Abstract

Recent developments in MS-based proteomics have increased the emphasis on peptides as a primary observable. While peptides are identified by tandem mass spectra, the link between peptide and protein remains implicit given the bottom-up nature of the experiment in which proteins are enzymatically digested prior to sequencing. It is therefore useful to provide a fast lookup from peptide to protein in order to systematically establish the broadest possible protein basis for the observed peptides. Here, we describe Pep2Pro, a fast web-service providing protein lookup by peptides covering the entire protein space comprising ∼10 million UniRef100 sequences. We demonstrate the usefulness of the service by reanalyzing peptides from two recent meta-proteomic data sets and identifying taxon-specific peptides, thereby implicating individual species as being present in these complex samples. The Pep2Pro web service can be accessed at http://www.pep2pro.org.