Specifying comet param file in batch file

[Mark Athanason]

Hello,

This may be a stupid question but I'm not great with windows batch processing. I'm trying to use Comet to search my MS files where a host of different PTMs will be present; as such, I'll need to specify these PTMs in various param files and perform the searches sequentially. Is there a way to direct comet to the specific param file I want rather than having several copies of comet.exe in the mxXML directory?

All the best,

Mark

[Jimmy Eng]

Mark,

You can specify an alternate parameters file to use using a command line option.  Type the Comet binary ("comet.exe" I presume) on the command line without any input arguments to get the usage statement with the command line options.  The "-P" option is to specify the parameter file e.g.

   comet.exe  -Palternate.parameters  inputfile.mzML

After each of your searches, you will have to rename your output files, e.g. inputfile.pep.xml, so that they are not overwritten with the subsequent search.  Is this what you're looking for?

Jimmy

[Mark Athanason]

Hi Jimmy,

Yes, that works! And I found the -N command to specify an output.

Thanks for the help,

Mark

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