Fast and Accurate Database Searches with MS-GF plus Percolator:  

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 identific...

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Bibliographic Details
Published in:Journal of proteome research 2014-02, Vol.13 (2), p.890
Main Authors: Granholm, Viktor, Kim, Sangtae, Navarro, José C. F., Sjölund, Erik, Smith, Richard D., Käll, Lukas
Format: Article
Language:English
Subjects:
Biochemistry towards Bioinformatics
bioinformatics
biokemi med inriktning mot bioinformatik
confidence estimation
machine learning
shotgun proteomics
Online Access:Get full text
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Summary: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.
ISSN:1535-3907
1535-3893
DOI:10.1021/pr400937n