crux tide-search

Usage:

crux tide-search [options] <mass spectra> <peptide index>

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.

To use crux tide-search, you must first create a database index using the crux tide-index command.

When tide-search runs, it performs several intermediate steps, as follows:

  1. Convert the given fragmentation spectra to a binary format.
  2. Search the spectra against the database and store the results in binary format.
  3. Convert the results to one or more requested output formats.
By default, the intermediate binary files are stored in the output directory and deleted when Tide finishes execution. If you plan to search a given set of spectra more than once, then you can direct Tide to save the binary spectrum files. Subsequent runs of the program will go faster if provided with inputs in binary format.

Input:

Output:

Options:


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