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.
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