Article "Speeding up Percolator" accepted for publication in Journal of Proteome Research

The article "Speeding up Percolator" by John T. Halloran, Hantian Zhang, Kaan Kara, Cedric Renggli , Matthew The, Ce Zhang, David M. Rocke , Lukas Käll and William Stafford Noble has been accepted for publication in the Journal of Proteome Research.


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 by using a machine learning post-processor. Here, we describe our efforts to speed up one widely used post-processor, 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.