I am currently working with PTMProphet in TPP version 6.3.3 for PTM localization. While PTMProphet successfully completes the task, I am encountering a significant number of warning messages in the console.
To provide some context, my workflow involves utilizing MSFragger as the search engine to convert raw files to mzML files and then searching against a database. For the modification parameters, I have set M 15.9949, N-term 42.1016, STC 299.123, and C 57.02146 as variable modifications, with no fixed modifications specified. Upon obtaining the pepXML file from MSFragger, I employed Percolator for PSM validation using the following settings: *--only-psms --no-terminate --post-processing-tdc*. The resulting pepxml file was then processed with PTMProphet using the command: *STC:299.123 MINPROB=0.5 MODPREC=0 FRAGPPMTOL=15 NOSTACK MAXTHREADS=1*. However, during the PTMProphet processing, I encountered warning messages similar to the following: *[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: S[386]CNGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD (SpectraST::Peptide) = S[386]CNGGSHPR Neutral Computed Mass for Evaluation = 1212.51 PPM difference = 33487.5[INFO:] please check your specified modification masses for precision or adjust MODPREC= parameter ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: SC[402]NGGSHPR Neutral Mass (from pepXML) = 1254.52 BAD (SpectraST::Peptide) = SC[402]NGGSHPR Neutral Computed Mass for Evaluation = 1212.51 PPM difference = 33487.5[INFO:] please check your specified modification masses for precision or adjust MODPREC= parameter ...[WARNING:] Illegal PTM-shuffled peptide detected with non-matching mass: SCNGGS[386]HPR Neutral Mass (from pepXML) = 1254.52 BAD (SpectraST::Peptide) = SCNGGS[386]HPR Neutral Computed Mass for Evaluation = 1212.51 PPM difference = 33487.5[INFO:] please check your specified modification masses for precision or adjust MODPREC= parameter ...* This pattern repeats for various peptides, indicating that PTMProphet is struggling to localize modifications on S, T, or C. The tool suggests adjusting parameters, specifically the MODPREC= parameter. Has anyone encountered a similar issue with PTMProphet and successfully addressed it? I would greatly appreciate any insights, advice, or suggestions regarding this matter. -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/ae1adab3-5501-4f29-b9d2-44d6252e7e84n%40googlegroups.com.
