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


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 an optional 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 21 amino acids. Peptides containing non-amino acid alphanumeric characters (BJXZ) are skipped. Non-alphanumeric characters are ignored completely.



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: