What it does

Runs multiple search engines on any number of MGF peak lists using SearchGUI.

Default: X! Tandem and MS-GF+ are executed.

Optional: MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.

Input FASTA

In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences) and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format:

>generic[your tag]|[protein accession]|[protein description]

or

>generic[your tag]|[protein accession]

See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta.