tide-index bullseye tide-search comet search-for-xlinks percolator barista q-ranker spectral-counts

Crux is a software toolkit for tandem mass spectrometry analysis. If you use Crux in your research, please cite

Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and William Stafford Noble. "Rapid and accurate peptide identification from tandem mass spectra." Journal of Proteome Research. 7(7):3022-3027, 2008.

For a more up-to-date description of Crux, please read

Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas, Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael J. MacCoss and William Stafford Noble. "Crux: rapid open source protein tandem mass spectrometry analysis." Journal of Proteome Research. 13(10):4488-4491, 2014.

Download Crux Toolkit

Crux is provided as a single executable that supports the following commands:

Primary commands
bullseye Assign high resolution precursor m/z values to MS/MS data using the Hardklör algorithm.
tide-index Create an index of all peptides in a fasta file, for use in subsequent calls to tide-search.
tide-search Search a collection of spectra against a sequence database, returning a collection of peptide-spectrum matches (PSMs). This is a fast search engine but requires that you first build an index with tide-index.
comet Search a collection of spectra against a sequence database, returning a collection of PSMs. This search engine runs directly on a protein database in FASTA format.
percolator Re-rank a collection of PSMs using the Percolator algorithm. Optionally, also produce protein rankings using the Fido algorithm.
q-ranker Re-rank a collection of PSMs using the Q-ranker algorithm.
barista Rank PSMs, peptides and proteins, assigning a confidence measure to each identification.
search-for-xlinks Search a collection of spectra against a sequence database, finding cross-linked peptide matches.
spectral-counts Quantify peptides or proteins using one of three spectral counting methods.
Utilities
calibrate-scores Assign two types of statistical confidence measures (q-values and posterior error probabilities) to each PSM in a given set.
make-pin Given a set of search results files, generate a pin file for input to crux percolator
predict-peptide-ions Given a peptide and a charge state, predict the m/z values of the resulting fragment ions.
hardklör Identify isotopic distributions from high-resolution mass spectra.
print-processed-spectra Process spectra as for scoring xcorr and print the results to a file.
generate-peptides Extract from a given set of protein sequences a list of target and decoy peptides fitting the specified criteria.
get-ms2-spectrum Extract one or more fragmentation spectra, specified by scan number, from an MS2 file.
version Print the Crux version number to standard output, then exit.
Utilities for processing tab-delimited text files
extract-columns Print specified columns from a tab-delimited file.
extract-rows Print specified rows from a tab-delimited file.
stat-column Collect summary statistics from a column in a tab-delimited file.
sort-by-column Sort a tab-delimited file by a column.

File formats

  bullseye tide-index tide-search comet percolator q-ranker barista search-for-xlinks spectral-counts
MS1 in                
MS2 (sample) / CMS2, MGF in/out   in in in in in in in
mzML, mzXML in   in in in in in in in
Thermo .raw files (Windows only) in   in in   in in in in
Other proprietary vendor formats (Windows only)     in     in in in in
FASTA (sample) in in   in       in  
database index   out in            
Tab-delimited text (sample)     out out in/out in/out in/out out in/out
pepXML     out out in/out out out   in
PIN     out   in        
POUT         out        
mzIdentML     out out out       in
SQT     out out in in in   in
Features         in/out out      
Barista XML             out    
Crux parameters (sample) in/out in/out in/out in/out in/out in/out in/out in/out in/out

Tutorials

Important links


The original version of Crux was written by Chris Park and Aaron Klammer under the supervision of Prof. Michael MacCoss and Prof. William Stafford Noble in the Department of Genome Sciences at the University of Washington, Seattle. The complete list of contributors can be found here.

Maintenance and development of Crux is funded by the National Institute of General Medical Sciences grants R01 GM096306 and P41 GM103533.


Please send comments and questions to cegrant@uw.edu.