Running CRUX

CRUX is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification.

CRUX (version 1.37) has been installed on lewis under /share/apps/crux/. All the executables and tools are in /share/apps/crux/bin/.

Users may include the CRUX executables/tools in the PATH by the following command so that they don't have to include the path in their commands to run the CRUX.

export PATH=$PATH:/share/apps/crux/bin

The command to run CRUX looks like this

crux <command> [options] <argument>

A sample LSF job script file to run CRUX on lewis may include the following lines:

#BSUB -J jobname
#BSUB -o jobname.o%J
#BSUB -e jobname.e%J

crux search-for-matches test.ms2 small-yeast.fasta

where "test.ms2" is a mass spectra input file and "small-yeast.fasta" is a sample protein database file in FASTA format.

Then, type the following command to submit the job on lewis

bsub < jobfile

This will generate a new deirectory named "crux-output" with seven new files, containing the search results output files.

For more information about how to submit jobs via LSF, please go to Submitting Jobs via LSF on Lewis.


 Usage: crux <command> [options] <argument>

crux supports the following commands:
  create-index             Create an index for all peptides in a fasta file.
  search-for-matches       Search a collection of spectra against a sequence database, 
                           returning a collection of peptide-spectrum matches (PSMs) 
                           scored by XCorr. 
  sequest-search           Similar to search-for-matches but use Sp as a preliminary 
                           score followed by XCorr. 
  compute-q-values         Assign a q-value, which is a statistical confidence measure 
                           that accounts for multiple testing, to each PSM in a 
                           given set 
  percolator               Analyze a collection of PSMs to target and decoy sequences 
                           using the percolator algorithm 
  q-ranker                 Analyze a collection of PSMs to target and decoy sequences 
                           using the q-ranker algorithm (marina's new q-ranker) 
  barista                  Protein identification algorithm that combines two different 
                           tasks — peptide-spectrum match (PSM) verification and 
                           protein inference — into a single learning algorithm. 
  print-processed-spectra  Write a new ms2 file with all of the same spectra with 
                           only the peaks used for computing xcorr. 
  search-for-xlinks        Search a collection of spectra against a sequence database 
                           returning a collection of matches corresponding to linear 
                           and cross-lnked peptides scored by XCorr. 
  spectral-counts          Rank proteins or peptides according to one of two quantification 
                           methods. 
  extract-columns          Prints a delimited file using only the columns specified 
                           from the original delimited file 
  extract-rows             Prints out rows that match a particular column value
  stat-column              Collects statistics from a column of data in a delimited 
                           file 
  sort-by-column           Sorts a delimited file by a column 
  version                  Print the Crux version number to standard output, then 
                           exit 

Options and arguments are specific to each command.Type 'crux <command>' for details.

For more information about how to use CRUX, see the CRUX Tutorials.