Hello Paul, You can get the instructions on using PTMProphet by running the tool on the commandline without any options. This applies to most of the commandline tools in the TPP.
When you type "*PTMProphetParser" *into the commandline, you'll get the following usage statement: *PTMProphetParser <OPTIONS> <input_file.pep.xml> [<output_file>]OPTIONS NOUPDATE Don't update modification_info tags in pepXML EM=<number>: Set EM models to <number> which can be 0, 1 or 2: 0 -> no EM, 1 -> Intensity EM Model Applied, 2 -> Intensity and Matched Peaks EM Models Applied (default=1) KEEPOLD Option to retain old PTMProphet results in the pepXML file (off by default). VERBOSE Option to produce WARNINGS to help troubleshoot potential PTM shuffling or mass difference issues (off by default). MZTOL=<number> Use specified +/- MS2 mz tolerance on site specific ions (default=0.1 dalton). PPMTOL=<number> Use specified +/- MS1 ppm tolerance on peptides which may have a slight offset depending on search parameters (e.g. iTRAQ4plex) (default=1 ppm). MINPROB=<number> Use specified minimum probability to evaluate peptides (default=0). MASSDIFFMODE Use the Mass Difference and localize MASSOFFSET=<number> Adjust the massdiff by offset <number> (default: 0) <amino acids, n, or c>:<mass_shift>:<neut_loss1>:...:<neut_lossN>,<amino acids, n, or c>:<mass_shift>:<neut_loss1>:...:<neut_lossN> Specify modifications (default: STY:79.9663:-97.97690:-115.9880,M:15.9949:-63.998286:-81.024835:-82.008850 )* If you have any issues running the software I would can help you understand them. Currently we are putting together a publication on PTMProphet, and more documentation will become available when that is accepted. There is still much to be done in understanding the optimal ways of localizing PTMs. Thanks for considering the TPP for your proteomics analysis needs. -David On Fri, Jan 5, 2018 at 7:29 AM, Paul Abraham <pabraham6...@gmail.com> wrote: > Hello, > > I am having a difficult time locating documentation for several of the TPP > tools. For example, the PTMProphet tool referenced on the wiki page does > not have any supporting documentation. Am I missing some obscure landing > page somewhere? The only information I find for how to efficiently utilize > this tool is by scouring this forum and this is by no means a good use of > time, considering most posts highlight the issues. > > Can anyone point to documentation for this tool particularly, but other > TPP tools as well? > > Regards, > Paul > -- > 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 post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
