Crux tandem mass spectrometry analysis software
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 | |
| 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). |
| sequest-search | Search a collection of spectra against a sequence database, similar to search-for-matches, but more closely mimicking the SEQUEST algorithm. |
| 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 | 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 q-value, 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 | Score peptides or proteins by one of three quantification methods. |
| Utilities | |
| print-processed-spectra | Process spectra as for scoring xcorr and print results to file. |
| generate-peptides | Given protein sequencs in a fasta file return a list of peptides fitting the specified criteria. |
| get-ms2-spectrum |
Extract one or more MS-MS spectra, specified by scan number, from
a .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 |
Crux frequently asked questions
Tide
This version of Crux is released with a demo version of a new search
engine, Tide. Tide is an independent
reimplementation of the SEQUEST algorithm. The immediate ancestor of
Tide is the Crux search-for-matches command, but Tide has
been completely re-engineered to achieve a thousandfold improvement in
speed while exactly replicating Crux XCorr scores. Currently, Tide is
not fully integrated with Crux, and is available only in binary
executable format.
- MS2 spectrum files (sample)
- FASTA sequence files (sample)
- Peptide database index files (binary)
- Text SQT files for representing PSMs. (sample)
- Text feature files for representing PSMs. (sample)
- Crux parameter files (sample)
Tutorials
- Installation
- Getting started with Crux
- Searching a protein database
- Creating a peptide index
- Customizing a search
Download
Two versions of Crux are available:
- You can download a fully functional version of Crux here once you agree to the license agreement and obtain a password here. The Crux source code is freely available for academic use and can be licensed for commercial use. Currently, a single-user license costs US $50.
- An open source version of Crux can be downloaded here. This version of Crux is covered by an Apache license. Due to intellectual property issues, this version of Crux has the search capability disabled, but all of the other Crux tools can be used in conjunction with a separate search engine.
To receive announcements of new versions, sign up for the Crux users mailing list.
For support, and to discuss Crux with other users and the developers, sign up for the Crux users Google group.
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.
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Maintenance and development of Crux is funded by the National Institute of Biomedical Imaging and Bioengineering grant NIH/NIBIB R01 EB007057 and by the National Center for Research Resources grant NIH/NCRR P41 RR0011823. |
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Please send comments and questions to cegrant@u.washington.edu.