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J Am Soc Mass Spectrom. 2016 Nov;27(11):1719-1727. Epub 2016 Aug 29.

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0.

Author information

1
Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden.
2
Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, 98195, USA.
3
Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195, USA.
4
Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden. lukas.kall@scilifelab.se.

Abstract

Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values and posterior error probabilities, to peptides and peptide-spectrum matches (PSMs) from such experiments. Percolator's processing speed has been sufficient for typical data sets consisting of hundreds of thousands of PSMs. With our new scalable approach, we can now also analyze millions of PSMs in a matter of minutes on a commodity computer. Furthermore, with the increasing awareness for the need for reliable statistics on the protein level, we compared several easy-to-understand protein inference methods and implemented the best-performing method-grouping proteins by their corresponding sets of theoretical peptides and then considering only the best-scoring peptide for each protein-in the Percolator package. We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license. Graphical Abstract ᅟ.

KEYWORDS:

Data processing and analysis; Large scale studies; Mass spectrometry - LC-MS/MS; Protein inference; Statistical analysis

PMID:
27572102
PMCID:
PMC5059416
DOI:
10.1007/s13361-016-1460-7
[Indexed for MEDLINE]
Free PMC Article

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