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 four 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.
  4. Pseudo quantitation using spectral-counts

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: