Crux tandem mass spectrometry analysis software

create-index bullseye search-for-matches search-for-xlinks barista percolator q-ranker calibrate-scores spectral-counts

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

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.
create-index Speed up subsequent searches by creating 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).
calibrate-scores Assign two types of statistical confidence measures (q-values and posterior error probabilities) to each PSM in a given set.
percolator Re-rank a collection of PSMs using the Percolator algorithm.
q-ranker Re-rank a collection of PSMs using the Q-ranker algorithm.
barista Rank proteins and assign a confidence measure to each protein 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.
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 peptides fitting the specified criteria.
get-ms2-spectrum Extract one or more MS/MS 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



Crux frequently asked questions

Crux Google Scholar profile

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For support, and to discuss Crux with other users and the developers, sign up for the Crux users Google group.

Release notes.

Known issues.

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.

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