Introduction

Crux is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux implements the Sequest algorithm and accelerates the search using a regenerated index file.

More information can be found at http://noble.gs.washington.edu/proj/crux/

Currently, the Crux-txt DAO supports spectra in MS2 format only.

Parameters

• Threshold: The maximum expect value a peptide may have to still be included in the PRIDE XML file. All peptides with an expect value greater than the set threshold will be ignored. Default value is 0.0.

• Decoy Prefix: allows adding a prefix to decoy hits that will be included in the Pride XML file.

• Score Criteria: the score criteria used to apply the Threshold filter. Default value is xcorr_rank.

• Get Highest Score Item: if true, only the highest scored peptide for a given spectrum will be included in the Pride XML file. Default value is true.

Details

• PTMs: Post-translational modifications are specified in the peptide sequence (variable modifications) and in the parameter file (variable modifications, fixed modifications, and terminal modifications).