I have run the TPP on MSFragger results, including iProphet, before. What parameters did you use for PeptideProphet? What was the output of that command? Is it possible that you don't have any high scoring PSM left after PeptideProphet filtering?
Thanks, -David On Mon, Oct 23, 2017 at 11:42 AM, Adam R <[email protected]> wrote: > Hi Everyone, > > I am running into a problem with iProphet when trying to perform > additional validation on PeptideProphet files sourced from MSFragger > pep.xml output. The command fails and > shows the warning "file not found: not created or deleted?" Has anyone > else had this issue before? I would like to be able to use MSFragger output > files (wide mass search) and feed the resulting output through > PeptideProphet/iProphet/PTMProphet. > > Thanks, > > Adam > > > -- > 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 https://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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
