crux sequest-search

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

This command searches a protein database with a set of spectra, using an algorithm similar to that employed by the SEQUEST database search software. This command differs from the crux search-for-matches command in the following respects:

Similar to crux search-for-matches, 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.

This command handles modifications in the same way as crux search-for-matches.

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 search.decoy.sqt and search.decoy.txt are also produced.

Options: Parameter file options:

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