I've run into an issue with PTMProphet where occasionally the command will fail for unknown reasons and the resulting ptm.pep.xml cannot be opened with the PepXML viewer. The command log seems to cut off abruptly, as pictured in the attached screenshot. Also attached is the page that appears upon trying to open the ptm.pep.xml.
The interact.pep.xml files we're analyzing clock in at about 200 to 250 megabytes. As a workaround, we currently just split the initial batch of pep.xmls into smaller groups before running PeptideProphet and PTMProphet on them again. Sometimes we end up with batches of pep.xmls as small as 3 or 4 files, which is somewhat inconvenient for projects with hundreds of RAW files.
Is there another way around this issue? We've tried running it through the command line as well and this problem still crops up frequently.