Hi everyone, I'm a bit confused about the workflow for finding PTMs. At first glance and seeing the code for xinteract, it seems it should be:
Search->PeptideProphet->InterProphet (apply 1% FDR)->PTMProphet However, looking at the code for PTMProphet, it uses the decoy hits to build its null distribution. So my intuition says the following workflow would be correct: Search->PeptideProphet->PTMProphet->InterProphet (apply 1% FDR) Because we want to have the false hits to build the null distribution in PTMProphet. Can anyone clarify these points? Thank you, Chris -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
