decoy proteins issue

[kusal bellana]

Hi, 

I'm having issues in TPP specifically with decoy proteins appearing in the top results after FDR filtering. For example in one of my ipro.prot.xml files I processed through the Petunia pipeline, there are 20 decoy proteins that are at 0.990 probability. I'm not sure what to do since I included "DECOY_" as the decoy prefix in my comet.params txt file as well as in my peptideprophet search. Suggestions would be appreciated.

Thanks,

Kusal