Dear Longping, Maybe you can compress your analysis pepXML and mzML files and post them somewhere so I can replicate the issue locally?
Meanwhile, you can try the specifying all variable mods used in the search, when you run PTMProphet by changing the modification string as follows: M:15.9949,n:42.1016,STC:299.123,C:57.02146 Cheers! -David On Fri, Nov 17, 2023 at 1:02 PM Longping Fu <lpf...@gmail.com> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/ae1adab3-5501-4f29-b9d2-44d6252e7e84n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAGJJY%3D-7EqZtHu2dDDDCUH%3D7-JkGHLSaLAQPxvhfa8D%2B%3D8JjKw%40mail.gmail.com.
