Dear all, I am encountering issues when trying to use PTMProphet on X!Tandem result files to validate phosphorylation sites.
Firstly, when converting the X!Tandem result files to pepXML using Tandem2XML, I get the error that the referred MGF file is not recognized *"Unknown file type. No file loaded.".*I checked that all the paths were correct. To overcome this issue I had to convert the original raw files in mzML for Tandem2XML to work, is it normal that MGF files are not supported ? Secondly, I get "*WARNING: Illegal PTM-shuffled peptide detected with non-matching mass*" warnings when running PTMProphet on the pepXML file. What I don't understand is that the difference in ppm that are given by the warnings are quite extreme (80000-150000 ppm). And even if I increase the MS1 tolerance enough using the PPMTOL parameter, no information is inserted in the "modification_info" tags in the produced XML file. Am I missing something obvious ? PS: I use command lines and the latest version of the TPP on linux mint (64 bits). Many thanks in advance, Thibault -- 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.
