crux search-for-xlinks

Usage:
crux search-for-xlinks [options] <ms2 input filename> <protein database> <link sites> <link mass>
Description:

This command searches a protein database with a set of spectra. For each spectrum, the precursor mass is computed from either the precursor singly charged mass (m+h) or the mass-to-charge (m/z) and an assumed charge. Candidates molecules are linear peptides, dead-end products, self-loop products or cross-linked products whose mass lies within a specified range of the precursor mass. These candidate peptides are ranked using XCorr. The input protein database is in FASTA format.

The algorithm is described in more detail in the following article:

Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. Goodlett and William Stafford Noble. "Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs." Journal of Proteome Research. 2010.

Modifications: Currently, crux search-for-xlinks supports static modifications (a change of mass applied to a given amino acid in every peptide in which it occurs). By default, a static modification of +57 Da to cysteine (C) is applied. Variable modifications (allowing peptides to be generated with and without a mass change to a given amino acid), are supported when use-old-xlink=F. Static and variable modifications can be specified in the parameter file, as described below.

Input:

Output:

The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created:

Options:


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