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

The Crux mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. The toolkit includes several search engines for both standard and cross-linked database search, as well as a variety of pre- and post-processing engines for assigning high-resolution precursor masses to spectra, assigning statistical confidence estimates to spectra, peptides and proteins, and performing label free quantification. Crux comes pre-complied for the Linux, Windows and MacOS operating systems. It is implemented as a single program that offers a wide variety of commands. 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.
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
param-medic Examine the spectra in a file to estimate the best precursor and fragment error tolerances for database search.
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.