Hello Zack, Each evaluated modification site gets a PTMProphet calculated probability of the modification being at that site. If you mouse over the bar you will get the value of the probability. You can export the results to xls file and the ptm_peptide column will show the values next to the evaluated site in parenthesis.
Cheers, -David On Fri, Jan 5, 2018 at 4:46 PM, Zack Potter <zackgra...@gmail.com> wrote: > Hi David, > > Thanks for posting the path to the PTMProphet documentation--was just > looking for it last night. > > After analyzing some data, and when viewing it in the PepXML viewer, what > is the significance of the colored boxes above the individual residues in > the PTMPeptide column? Despite the documentation, I've still not figured > out what they mean. > > Best, > -Zack > > On Friday, January 5, 2018 at 9:39:03 AM UTC-8, 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> 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. >>> To post to this group, send email to spctools...@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. > -- 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.
