Hi Paul, It sounds like what you are looking for is the MASSDIFFMODE option in PTMProphet. You can run MASSDIFFMODE on MSFragger results and it will localize the mass difference of each ID like a PTM. You should set MZTOL= parameter to be consistent with the mass accuracy of your dataset on the MS2 level. If it gives you any issues as far as warnings or errors please let me know and I can help you troubleshoot.
Thanks, -David On Fri, Jan 5, 2018 at 11:07 AM, Paul Abraham <[email protected]> wrote: > 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 <[email protected]> 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 [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
