Fragpipe

[cutleraging]

Hello,

Is there any support for using fragpipe results?

Best,
Ronnie

[MatthewThe]

Hi Ronnie,

We have started work on this but unfortunately it isn't ready just yet. We will keep you updated, or please let us know if you have an interest in helping to add this feature.

[cutleraging]

Hi Matthew,

I would be interested in helping to add this. I assume if I can get all of the same information from the fragpipe PSM files that you usually get from the MaxQuant evidence files, then it should theoretically be able to work on the fragpipe output?

Ronnie

[fhamood]

Hi Ronnie,

Yes, in the end, the easiest approach would be to build files that resemble the MaxQuant "msms.txt", "msmsScans.txt", "allPeptides.txt", and "evidence.txt" files. In the respective functions in maxquant.py you can see which columns are used, specifically. If you can add a script that builds those tables from FragPipe output files then that would be a great help.

Firas