The complete peptide dictionary – A meta‐proteomics resource

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