crux search-for-matches

Usage:
crux search-for-matches [options] <ms2 input filename> <protein input>
Description:

This command searches a protein database with a set of spectra. For each spectrum, the precursor mass is computed from either the measured precursor singly charged mass (m+h) or the mass-to-charge (m/z) and an assumed charge. Candidate peptides whose mass lies within a specified range of the precursor mass are identified. These candidate peptides are scored with the SEQUEST® XCorr, and the top-ranking matches for each spectrum are reported.

An optional p-value may be computed for each spectrum based on the distribution of scores for that spectrum ( Aaron A. Klammer, Christopher Y. Park and William Stafford Noble. "Statistical calibration of the SEQUEST XCorr function." Journal of Proteome Research. 8(4):2106-2113, 2009).

The input protein database may either be in FASTA format or it may be a binary index created by crux create-index. Using an index will typically yield much faster search speeds.

Modifications: Crux handles two types of modifications: static and variable. Static modifications are 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 cystine (C) is applied. Variable modifications allow peptides to be generated with and without a mass change to a given amino acid. Crux handles variable modifications as follows. The user specifies an allowed set of amino acid modifications, using the options mod, cmod and nmod, which are described below. Before any search is performed, Crux generates an exhaustive list of all possible combinations of amino acid modifications that could be applied to a peptide. Subsequently, for each spectrum, Crux performs one search for each possible combination of modifications including no modifications. For example, if the precursor m/z for a spectrum is 800 Th, the charge state is 2+, and Crux is considering a modification of +79, then Crux will retrieve from the database all candidate peptides whose total mass is close to 321 Th. The candidate peptide list is then updated to remove any peptides that cannot be modified (because they contain no modifiable amino acids) and expanded to include all possible modified forms of each candidate. These candidates are scored as usual and the top n candidate peptides are added to a composite, sorted list of peptides. Finally, after all modifications have been searched, Crux reports for the current spectrum the top m peptides from the composite list.

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:

If decoys are enabled using --num-decoys-per-target, then files called search.decoy.txt and search.decoy.pep.xml are also produced.

Options: Parameter file options:

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