crux pipeline [options] <mass spectra> <peptide source>


Given one or more sets of tandem mass spectra as well as a protein database, this command runs a series of Crux tools and reports all of the results in a single output directory. There are three steps in the pipeline:

  1. Bullseye to assign high-resolution precursor m/z values to MS/MS data. This step is optional.
  2. Database searching using either Tide-search or Comet. The database can be provided as a file in FASTA format, or additionally, an index as produced by tide-index.
  3. Post-processing using either assign-confidence or Percolator.

All of the command line options associated with the individual tools in the pipeline can be used with the pipeline command.



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: