Brian and David, Thank you for chiming in. Yes, I am aware of the "--help" option that is available. I was hoping to get a better understanding of PTMprophet in particular, so thank you for highlighting the upcoming publication. In regards to PTMProphet, I'd like to use this in conjunction with MSFragger open-search specifically. Can localization be done for the collection of mods (mass shifts) identified by MSFragger or is PTMProphet limited to a pre-defined mass shift list, in which the modifications have to be specified upfront.
I should note that I am using the Philosopher software and using PTMProphet in between PeptideProphet and ProteinProphet. Thanks, Paul On Friday, January 5, 2018 at 12:39:03 PM UTC-5, David Shteynberg wrote: > > 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 <pabrah...@gmail.com > <javascript:>> 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-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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.
