crux q-ranker

Description:

Q-ranker dynamically learns to separate target from decoy PSMs. The algorithm is described in this article:

Marina Spivak, Jason Weston, Leon Bottou and William Stafford Noble. "Direct q value optimization methods for peptide identification from shotgun proteomics data sets." Journal of Proteome Research. 8(7):3737-3745, 2009.

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

Usage:

crux q-ranker [options] <spectra> <search results>

Required Input:

Output: Options:

Selected Examples of Use:


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