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/binThe 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 jobnamewhere "test.ms2" is a mass spectra input file and "small-yeast.fasta" is a sample protein database file in FASTA format.
#BSUB -o jobname.o%J
#BSUB -e jobname.e%J
crux search-for-matches test.ms2 small-yeast.fasta
Then, type the following command to submit the job on lewis
bsub < jobfileThis 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.