crux cascade-search [options] <tide spectra file> <database-series>


Cascade-search is a general procedure for incorporating information about peptide groups into the database search and confidence estimation procedure. Peptides may be grouped according to, for example, their enzymatic properties (zero, one, or two enzymatic termini) or the presence of different types of numbers of variable modifications. The algorithm works on a series of databases, each corresponding to a different peptide group. The database is searched in series, and after each search, any spectrum that is identified with a user-specified confidence threshold is sequestered from subsequent searches. The full cascade search procedure is described in this article:

Attila Kertesz-Farkas, Uri Keich and William Stafford Noble. "Tandem mass spectrum identification via cascaded search." Journal of Proteome Research. 14(8):3027-38, 2015.



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: