crux tide-index

Usage:

crux tide-index [options] <protein input file> <index name>

Description:

Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST® algorithm, which assigns peptides to spectra by comparing the observed spectra to a catalog of theoretical spectra derived from a database of known proteins. Tide's primary advantage is its speed. Our published paper provides more detail on how Tide works. If you use Tide in your research, please cite:

Benjamin J. Diament and William Stafford Noble. “Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra.Journal of Proteome Research. 10(9):3871-9, 2011.

The tide-index command performs a required pre-processing step on the protein database, converting it to a binary format suitable for input to the tide-search command.

Tide considers only the standard set of 20 amino acids. Peptides containing non-amino acid alphanumeric characters (BJOUXZ) are skipped. Non-alphanumeric characters are ignored completely.

Input:

Output:

Options:


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