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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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MSGF+ Training parameter location #56

Closed mrForce closed 5 years ago

mrForce commented 5 years ago

I trained a param file using ScoringParamGen. The documentation says to place the param file (in my case, named HCD_QExactive_NoCleavage_Automatic.param) into a folder called "params". Should this folder by placed in the MSGF+ installation (in the same directory as MSGFPlus.jar), or in the directory that the search is being ran from?

Additionally, if I'm trying to train on a search done with "-e 0" (unspecific cleavage), what enzyme should I use for ScoringParamGen?

FarmGeek4Life commented 5 years ago

The folder should go in the working directory, i.e. the directory the command line says you are currently in before you enter 'java -Xmx... -jar MSGFPlus.jar ...'

mrForce commented 5 years ago

Perfect, thanks. I really appreciate you guys answering my questions. Though what should I do if I want to train params on a search done with unspecific cleavage, as there doesn't appear to be an option for that (the MSGF+ documentation says this: -e EnzymeID (0: Trypsin, 1: Chymotrypsin, 2: Lys-C, 3: Lys-N, 4: glutamyl endopeptidase, 5: Arg-C, 6: Asp-N, 7: alphaLP, 8: no cleavage); there's no option for unspecific cleavage)?