Chris, You must be looking at a non-functioning section of the code. PTMProphet relies only on the MS/MS spectrum information to determine the PTM site scores. PTMProphet assumes the identification is the correct peptide and attempts to find the most likely sites for the PTMs. It will work on any pepXML input file if run on the commandline, so either way of using the tool is fine.
Cheers, -David On Wed, Jun 4, 2014 at 6:42 AM, Chris <[email protected]> wrote: > 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. > -- 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.
