crux barista

Description:

Barista is a protein identification algorithm that combines two different tasks—peptide-spectrum match (PSM) verification and protein inference—into a single learning algorithm. The program requires three inputs: a set of MS2 spectra, a protein database, and the results of searching the spectra against the database. Barista produces as output three ranked lists of proteins, peptides and PSMs, based on how likely the proteins and peptides are to be present in the sample and how likely the PSMs are to be correct. Barista can jointly analyze the results of multiple shotgun proteomics experiments, corresponding to different experiments or replicate runs.

Barista uses a machine learning strategy that requires that the database search be carried out on target and decoy proteins. The searches may be carried out on a concatenated database or, using the --separate-searches option, separate target and decoy databases. The crux create-index command can be used to generate a decoy database.

Barista assigns two types of statistical confidence estimates, q-values and posterior error probabilities, to identified PSMs, peptides and proteins. For more information about these values, see the documentation for calibrate-scores.

Usage:

crux barista [options] <protein-database> <spectra> <search results>

Required Inputs:

Output: Options:

Selected Examples of Use:


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