Crux tandem mass spectrometry analysis software

Download Crux Toolkit

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.

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, provided either as a FASTA file or an index, returning a collection of peptide-spectrum matches (PSMs). This is a fast search engine, but it runs most quickly if provided with a peptide index built with tide-index.

cascade-search An iterative procedure for incorporating information about peptide groups into the database search and confidence estimation procedure.

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 and assign confidence estimates to 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.

pipeline Given one or more sets of tandem mass spectra as well as a protein database, this command runs a series of Crux tools and reports all of the results in a single output directory.

Utilities

assign-confidence Assign statistical confidence measures to each PSM in a given set.

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.

hardklör Identify isotopic distributions from high-resolution mass spectra.

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.

print-processed-spectra Process spectra as for scoring xcorr and print the results to a file.

psm-convert Convert a file containing peptide-spectrum matches (PSMs) from one format to another.

subtract-index Subtract one index file from another, assuming both were generated by tide-index.

xlink-assign-ions Given a spectrum and a pair of cross-linked peptides, assign theoretical ion type labels to peaks in the observed spectrum.

xlink-score-spectrum Takes a defined cross-linked peptide, a spectra file, and a scan number, and will calculate the XCorr score a number of different ways.

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 in/out in in in in in in in

MGF in/out 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 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

Feature file 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

Installation

Getting started with Crux

Running a simple search using Tide and Percolator

Customization and search options

Using spectral-counts

Important links

Crux frequently asked questions

Glossary of terminology

A graphical user interface for the Crux search tools, as well as a variety of other search tools, is available through SearchGUI. The sister program, PeptideShaker provides a way to combine the results of multiple search engines in the analysis of a single data set.

Crux Google Scholar profile

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.

Follow the Crux project on Sourceforge. The "Issues" list on Sourceforge includes known bugs as well as planned new features.

Access the most recent source code from the Crux main development trunk using the following Subversion command:
svn checkout svn://svn.code.sf.net/p/cruxtoolkit/code/crux/trunk crux-trunk

Release notes.

Crux is covered by an Apache license.

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 Institutes of Health awards R01 GM096306 and P41 GM103533.

Please send comments and questions to crux-developers@uw.edu or crux-users@googlegroups.com.

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, provided either as a FASTA file or an index, returning a collection of peptide-spectrum matches (PSMs). This is a fast search engine, but it runs most quickly if provided with a peptide index built with `tide-index`.
cascade-search	An iterative procedure for incorporating information about peptide groups into the database search and confidence estimation procedure.
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 and assign confidence estimates to 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.
pipeline	Given one or more sets of tandem mass spectra as well as a protein database, this command runs a series of Crux tools and reports all of the results in a single output directory.
Utilities
assign-confidence	Assign statistical confidence measures to each PSM in a given set.
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.
hardklör	Identify isotopic distributions from high-resolution mass spectra.
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.
print-processed-spectra	Process spectra as for scoring xcorr and print the results to a file.
psm-convert	Convert a file containing peptide-spectrum matches (PSMs) from one format to another.
subtract-index	Subtract one index file from another, assuming both were generated by tide-index.
xlink-assign-ions	Given a spectrum and a pair of cross-linked peptides, assign theoretical ion type labels to peaks in the observed spectrum.
xlink-score-spectrum	Takes a defined cross-linked peptide, a spectra file, and a scan number, and will calculate the XCorr score a number of different ways.
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.