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Nesvilab / PTM-Shepherd

A tool for summarizing open search results
http://ptmshepherd.nesvilab.org
Apache License 2.0
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Questions for PTM-Shepherd running #12

Closed YSosu closed 3 years ago

YSosu commented 3 years ago

Dear All,

I was analyzing tims tof pro data with MS Fragger, But I forgot to turn PTM-Shepherd on. So I want to run it with standalone mode. My question is when we are building config file it does required to add the directory for MZML file. In this case, Do I have to put the location of the raw data? or Either MGF or MZBINE files generated from MS Fragger?

Thanks,

fcyu commented 3 years ago

You can uncheck all other tools in FragPipe to make it only run PTM-Shepherd, which, I think, it the easiest way.

Best,

Fengchao

YSosu commented 3 years ago

Thanks, however, It says "Fatal error: In data set "q" could not find mzData for run XXXX. Does it say that because I have space in the directory of my file?

YSosu commented 3 years ago

I solved the problem by relocating the datafile to where there was no space in the directory

Thanks