Jeff Jones comments

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                                            Jeff Jones

Comet -- Error: No index found for enzyme Trypsin.

Thanks for the immediate response. Interesting. Apologies, where can I find that in the documentation? If I set the values to "Trypsin_(no_P_rule)" such that ... "digestionParameters": { "cleavageParameter": "enzyme", "enzymes":...

Comet -- Error: No index found for enzyme Trypsin.

Ahh! Typo. Missing the ")", Seems to work fine now for Tide and others ... ... "nMissedCleavages": { "Trypsin_(no_P_rule": 2 }, Thanks for the feedback. Still looking for the SearchCLI...

Comet -- Error: No index found for enzyme Trypsin.

Interesting. Most the other algorithms accept Trypsin_(no_P_rule), except Comet, I noticed Tide also has a warning. java -cp SearchGUI-4.3.1.jar eu.isas.searchgui.cmd.SearchCLI -id_params trypNoP3ptm_0.1Da.par .. -comet 1 -tide 1 Thu Oct 19...

Comet -- Error: No index found for enzyme Trypsin.

The specificity is in using no underscore for "Trypsin (no P rule)". That seems to work with SearchCLI now for all algorithms.