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Speeding Up Percolator
Speeding Up Percolator
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- Halloran, John T. (author)
- Univ Calif Davis, Dept Publ Hlth Sci, Davis, CA 95616 USA.
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- Zhang, Hantian (author)
- Swiss Fed Inst Technol, Dept Comp Sci, CH-8092 Zurich, Switzerland.
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- Kara, Kaan (author)
- Swiss Fed Inst Technol, Dept Comp Sci, CH-8092 Zurich, Switzerland.
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- Renggli, Cedric (author)
- Swiss Fed Inst Technol, Dept Comp Sci, CH-8092 Zurich, Switzerland.
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- The, Matthew (author)
- KTH,Science for Life Laboratory, SciLifeLab
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- Zhang, Ce (author)
- Swiss Fed Inst Technol, Dept Comp Sci, CH-8092 Zurich, Switzerland.
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- Rocke, David M. (author)
- Univ Calif Davis, Dept Publ Hlth Sci, Davis, CA 95616 USA.
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- Käll, Lukas, 1969- (author)
- KTH,Science for Life Laboratory, SciLifeLab
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- Noble, William Stafford (author)
- Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA.;Univ Washington, Paul Allen Sch Comp Sci & Engn, Seattle, WA 98195 USA.
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Univ Calif Davis, Dept Publ Hlth Sci, Davis, CA 95616 USA Swiss Fed Inst Technol, Dept Comp Sci, CH-8092 Zurich, Switzerland. (creator_code:org_t)
- 2019-08-13
- 2019
- English.
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In: Journal of Proteome Research. - : AMER CHEMICAL SOC. - 1535-3893 .- 1535-3907. ; 18:9, s. 3353-3359
- Related links:
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https://www.ncbi.nlm...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- The processing of peptide tandem mass spectrometry data involves matching observed spectra against a sequence database. The ranking and calibration of these peptide-spectrum matches can be improved substantially using a machine learning postprocessor. Here, we describe our efforts to speed up one widely used postprocessor, Percolator. The improved software is dramatically faster than the previous version of Percolator, even when using relatively few processors. We tested the new version of Percolator on a data set containing over 215 million spectra and recorded an overall reduction to 23% of the running time as compared to the unoptimized code. We also show that the memory footprint required by these speedups is modest relative to that of the original version of Percolator.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Keyword
- tandem mass spectrometry
- machine learning
- support vector machine
- SVM
- percolator
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Halloran, John T ...
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Zhang, Hantian
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Kara, Kaan
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Renggli, Cedric
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The, Matthew
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Zhang, Ce
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show more...
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Rocke, David M.
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Käll, Lukas, 196 ...
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Noble, William S ...
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
- Articles in the publication
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Journal of Prote ...
- By the university
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Royal Institute of Technology