Config file neeed

[ypriverol]

Dear @alchemistmatt @FarmGeek4Life:

Moving towards integration of MSGF+ with other systems would be great to have a parameters file for all MSGF+ parameters.(perhaps excluding in file and output file). do you think that is possible, are you accepting PR around that?

[alchemistmatt]

We would definitely accept a pull request for that. Regarding the parameter file format, we already have one that we use internally, so if you could adopt that format it would be a win for us too. Our internal system (C# code base) reads the parameter file and converts the settings to the command line arguments. Having Java code inside MS-GF+ read the parameter file would be an improvement. See these links for some example parameter files.

• MSGFDB_Tryp_DynMetOx_TMTExclusive_K_Acetyl_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
• MSGFDB_Tryp_DynSTYPhos_Stat_CysAlk_iTRAQ_4Plex_10ppmParTol.txt
• MSGFDB_PartTryp_Dyn_MetOx_CysAlk_20ppmParTol.txt

The code also converts the dynamic and static mods specified in the parameter file to create a file like MSGFPlus_Mods.txt (next bullet). However, for the new code you're proposing, this file shouldn't need to be created; just load the mod info into memory when reading the parameter file.

• MSGFPlus_Mods.txt

For reference, the C# code that parses these parameter files is at https://github.com/PNNL-Comp-Mass-Spec/DMS-Analysis-Manager/blob/master/Plugins/AM_MSGFDB_PlugIn/clsMSGFPlusUtils.cs#L2079 using this mapping: https://github.com/PNNL-Comp-Mass-Spec/DMS-Analysis-Manager/blob/master/Plugins/AM_MSGFDB_PlugIn/clsMSGFPlusUtils.cs#L1133

[ypriverol]

I think it make sense to provide a config file that contains also the modifications in the same format they were provided before but only one file. Working with your examples now.

[ypriverol]

First implementation provided in the following PR https://github.com/MSGFPlus/msgfplus/pull/59

[ypriverol]

The PR has been integrated and the current version of MSGF+ support config files. I will close this Issue.