MSstats without evidence.txt

[Lincoln Harris]

Hi, 

I'm trying to run MSstats on a PRIDE dataset that has been processed with MaxQuant (PXD014156). This project provides the proteinGroups.txt file, but not evidence.txt. I'm wondering if its possible to run MSstats without the MaxQuant evidence file, for this experiment? 

Thanks, 

Lincoln 

[Devon Kohler]

Hi Lincoln,

Unfortunately the MaxQuant converter requires the evidence.txt file. This is because we work on the PSM level and the proteinGroups.txt file does not contain the information we need.

Best,

Devon

[Lincoln Harris]

Thanks for the info!