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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Pause point between generating .pepXML and .pin file #1813

Closed bingnanzhao closed 2 hours ago

bingnanzhao commented 2 hours ago

**- Hi Fragpipe team: I tried to open the MSFragger search result (XXX.rank1.pepXML) as a pandas dataframe, and made some midifications based on my criteria. I want to write it back to .pepXML format and proceed downstream modules. The question I have now is: 1) could you provide the schema of .pepXML file so that I can write it back to the format MSFragger need, 2) Could you also make a pause point right before generating .pin file for validation module, so that once I upload my modified .pepXML it will successfully proceed? I know this is not a popular request, but if you could just provide me some instruction on this it would be helpful.

Thanks, Bingnan **

fcyu commented 2 hours ago

1) could you provide the schema of .pepXML file so that I can write it back to the format MSFragger need

http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML

2) Could you also make a pause point right before generating .pin file for validation module, so that once I upload my modified .pepXML it will successfully proceed?

Unfortunately no.

If you have project specific feature request for MSFragger or FragPipe, please contact us by email for the protentional collaboration.

Best,

Fengchao

anesvi commented 2 hours ago

I think you should modify the pin file. Then you can just rerun from msbooster or percolator.

bingnanzhao commented 2 hours ago

Thanks Fengchao and prof. Nesvizhskii,

Thanks for your suggestions and I believe we will formally collaborate on this later some time! Prof. Nesvizhskii just propose a very helpful suggestion and I will definitely try to work on .pin file directly. Just one last question remains on this: can I put the modified pin file in the work directory as a .csv file for proceeding msbooster or percolator?

Thanks, Bingnan

yangkl96 commented 2 hours ago

You can save the modified pin file as a tsv file, but make sure to keep the same name as the original pin files, including the .pin extension

bingnanzhao commented 2 hours ago

Got it that would be very helpful! Thanks you all!

Best, Bingnan

fcyu commented 1 hour ago

The modified file should have the pin extension and the columns separated with tab. Also remember to uncheck/disable the MSFragger tab when you run it the second time, otherwise, MSFragger will overwrite your pin files.

Best,

Fengchao

bingnanzhao commented 1 hour ago

Thanks so much Fengchao, I will try this very quickly and hopefully it would work!

Thanks, Fengchao