Dear David, Thank you for providing your suggestions. I implemented your advice by including all variable modifications in the search, and the warning messages did not appear.
I appreciate your assistance. Sincerely, Longping 在2023年11月17日星期五 UTC-5 20:49:25<David Shteynberg> 写道： > Thanks Longping, I got your files. > > On Nov 17, 2023, at 5:21 PM, Longping Fu <lpf...@gmail.com> wrote: > > Dear David, > > I appreciate your swift response. I've compressed the pepXML and mzML > files and uploaded them to Google Drive. You can access them through the > following link: > https://drive.google.com/file/d/1P463uxdvw67ZI7axiZO1OZOIlEZZg5qh/view?usp=sharing > > Kindly confirm if you can successfully open the files. > > Additionally, I'll be following your suggestion to include all variable > modifications and check for any remaining warning messages. > > Thank you for your assistance. > > Sincerely, > Longping > > 在2023年11月17日星期五 UTC-5 16:20:11<David Shteynberg> 写道： > > 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-discu...@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-discu...@googlegroups.com. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/27485be2-f0b5-411e-a4e7-13cc49e588d5n%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/27485be2-f0b5-411e-a4e7-13cc49e588d5n%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/6cbf03eb-374e-4f87-a255-5f642f548960n%40googlegroups.com.
