which column to use for mokapot generated rescoring results?

[frankligy]

Hello,

Sorry I have another question, so for the mokapot generated results, I usually look for the ms2rescore.mokapot.psms.txt, based on my understanding of the output, I was planning to use the column called "mokapot q-value" such that If I use FDR 5%, then I should retain ones with this column less than 0.05, because that's the definition of q-value right?

But I also saw the mokapot score and seems the generated figure cut off at 0, and there's also a PEP column, so just want to confirm with you how would you interpret the mokapot result and to filter based on a defined FDR.

Thank you,
Frank