Crux tandem mass spectrometry analysis software

One of the major challenges in proteomics is to identify the proteins that are expressed in cells under different conditions. Mass spectrometry is a widely used method for protein identification; however, a detailed spectrum analysis is required to match the spectrum to the source protein. Crux contains software for tandem mass spectrometry analysis, with a focus on peptide identification. It can be downloaded here once you agree to the license agreement and obtain a password here. Crux source code is freely available for academic use and can be licensed for commercial use. Crux optionally makes use of the Percolator algorithm (v. 1.3), which can be downloaded separately here.

The core programs in the Crux toolkit are

• crux-search-for-matches Search a collection of spectra against a sequence database, returning a collection of peptide-spectrum matches (PSMs).
• crux-create-index Create an index for all peptides in a fasta file.
• crux-analyze-matches Analyze a collection of PSMs using one the Crux supported post-processing algorithms.

In addition, Crux contains the following utilities:

• crux-predict-peptide-ions Given a peptide and a charge state, predict the ions according to the provided options.
• crux-generate-peptides Given protein sequencs in a fasta file return a list of peptides fitting the specified criteria.
• crux-score-peptide-spectrum Score a single spectrum for matches to a list of peptides.
• crux-get-ms2-spectrum Extract an MS-MS spectrum with a specified scan number from a .ms2 file.
• spectacle Create an image file of an annotated spectrum.

A tutorial for installing and using the above programs can be found here.

Crux is written in C by Chris Park and Aaron Klammer under the supervision of Prof. William Stafford Noble in the Department of Genome Sciences at the University of Washington, Seattle. Development of Crux is supported by National Institutes of Health award R01 EB007057.