crux percolator

Usage:

crux percolator [options] <protein input> <search results directory>

Description:

Percolator is a semi-supervised learning algorithm that dynamically learns to separate target from decoy PSMs. The algorithm is described in this article:

Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and Michael J. MacCoss. "Semi-supervised learning for peptide identification from shotgun proteomics datasets." Nature Methods. 4(11):923-925, 2007.

For more on q-values and posterior error probabilities (PEP), see the documentaion for calibrate-scores.

Crux now includes code from Percolator 1.05. The current version of Percolator can be downloaded here. External versions of Percolator can be applied to the output of the Crux tools, but won't be used by the crux percolator command.

Percolator requires as input two collections of PSMs, one set derived from matching observed spectra against real ("target") peptides, and a second derived from matching against "decoy" peptides. Crux generates these decoys on the fly. Percolator will also accept a second set of decoy PSMs and use one set in training and one in calculating q-values. Producing two sets of decoy PSMs is the search-for-matches default behavior.

The features used by percolator to represent each PSM are summarized here.

Input:

Output: Options:
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