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The complete peptide dictionary – A meta-proteomics resource

Authors

  • Manor Askenazi,

    1. Department of Biological Chemistry, The Hebrew University of Jerusalem, Israel
    2. Departments of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
    3. Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
    4. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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  • Jarrod A. Marto,

    1. Departments of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
    2. Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
    3. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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  • Michal Linial

    Corresponding author
    1. Department of Biological Chemistry, The Hebrew University of Jerusalem, Israel
    • Department of Biological Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel Fax: +972-2-6586448
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  • Colour Online: See the article online to view Fig. 2 in colour.

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

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