U.S. Department of Energy

Pacific Northwest National Laboratory

Fast and accurate database searches with MS-GF+Percolator.

TitleFast and accurate database searches with MS-GF+Percolator.
Publication TypeJournal Article
Year of Publication2014
AuthorsGranholm V, Kim S, Navarro JCF, Sjölund E, Smith RD, Käll L
JournalJ Proteome Res

One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.

Alternate JournalJ. Proteome Res.
PubMed ID24344789
PubMed Central IDPMC3975676
Grant ListP41 GM103493 / GM / NIGMS NIH HHS / United States
Area of Research: 
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