kojak

Usage:

crux kojak [options] <input spectra>+ <protein database>

Description:

Kojak is a database search tool for the identification of cross-linked peptides from mass spectra. This search engine was developed and is maintained by Michael Hoopmann at the Institute for Systems Biology. Additional information about Kojak can be found at kojak-ms.org.

If you use Kojak, please cite:

"Kojak: Efficient analysis of chemically cross-linked protein complexes." Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. J Proteome Res 2015 May 1. doi: 10.1021/pr501321h

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: