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Brief Communication

Nature Methods 4, 923–925 (1 November 2007) | doi:10.1038/nmeth1113

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Lukas K|[auml]|ll , Jesse D Canterbury , Jason Weston , William Stafford Noble & Michael J MacCoss

Shotgun proteomics uses liquid chromatography–tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of confident peptide identifications from a collection of tandem mass spectra.