Speeding up Percolator

John T. Halloran, Hantian Zhang, Kaan Kara, Cédric Renggli, Matthew The, Ce Zhang, David M Rocke, Lukas Käll, William Stafford Noble

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)3353-3359
Number of pages7
JournalJournal of Proteome Research
Issue number9
StatePublished - Sep 6 2019


  • machine learning
  • percolator
  • support vector machine
  • SVM
  • tandem mass spectrometry

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)


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