Hi Adam, I am glad you figured out how to use it. If you run the tool run on the commandline without options, it will give you the usage statement.
I believe that the warning you saw comes from a bug with massdiffmode when it encounters a modification that is unrecognized (unspecified in the search and unknown mod not part of the list of mods). This type of error could occur if you run PTMProphet in massdiffmode on a file already processed with PTMProphet in massdiffmode. It should not affect the other results, however, I have created a new binary which will hopefully provide you with more information regarding the offending mod. Please try the following binary: https://www.dropbox.com/s/c8o6i6yqe6h33u4/PTMProphetParser.exe?dl=0 , rename your existing copy in C:\TPP\bin\PTMrophetParser.exe and copy the file from the link to C:\TPP\bin. Let me know what new (or old) error messages it gives you. Thank you. Cheers, -David On Thu, Sep 28, 2017 at 7:34 AM, Adam R <[email protected]> wrote: > Hi David, > > I attempted a run with PTMProphet with MASSDIFFMODE (I wasn't not sure > what the usage is for this feature, I looked at the source code on > sourceforge and did a best guess: is there a file outlining the different > usages of optional features somewhere online?) and ran with the > ipro.pep.xml file that I generated from the wide tolerance comet search. I > received several warnings back but the .ptm.pep.xml file was written and I > can see peptides with assigned sites of modifcation. Just wondering if > these warnings mean that some mods were not written to the output file? Is > there anything missing in the MASSDIFFMODE command that I should include? > > Best, > > Adam > > >PTMProphetParser MZTOL=0.2 MASSDIFFMODE > >interact_widetol_minus_saha_2.ipro.pep.xml > interact_widetol_minus_saha_2.ptm.pep.xml > INFO: Reading file interact_widetol_minus_saha_2.ipro.pep.xml ... > INFO: processed 500/8911 spectrum_queries. > INFO: processed 1000/8911 spectrum_queries. > INFO: processed 1500/8911 spectrum_queries. > INFO: processed 2000/8911 spectrum_queries. > INFO: processed 2500/8911 spectrum_queries. > INFO: processed 3000/8911 spectrum_queries. > INFO: processed 3500/8911 spectrum_queries. > INFO: processed 4000/8911 spectrum_queries. > INFO: processed 4500/8911 spectrum_queries. > INFO: processed 5000/8911 spectrum_queries. > INFO: processed 5500/8911 spectrum_queries. > INFO: processed 6000/8911 spectrum_queries. > INFO: processed 6500/8911 spectrum_queries. > INFO: processed 7000/8911 spectrum_queries. > INFO: processed 7500/8911 spectrum_queries. > INFO: processed 8000/8911 spectrum_queries. > INFO: processed 8500/8911 spectrum_queries. > Iterating PTM Model: ....5.done > INFO: Writing file interact_widetol_minus_saha_2.ptm.pep.xml ... > INFO: Reading file interact_widetol_minus_saha_2.ipro.pep.xml ... > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > L[113]IEKGLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > I[113]EKGLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > E[129]KGLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > K[128]GLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > L[113]R > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > R[156] > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > L[113]IEKGLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > I[113]EKGLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > E[129]KGLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > K[128]GLR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > WARNING: Illegal PTM-shuffled peptide detected with non-matching mass: > G[57]LR > Neutral Mass (from pepXML) = 827.487 > Neutral Computed Mass for Evaluation = 827.523 > PPM difference = 43.9714 > > > On Tuesday, September 26, 2017 at 5:50:48 PM UTC-5, David Shteynberg wrote: >> >> MASSDIFFMODE should be compatible with most pepXML files from comet and >> beyond. The only issue I see with using SpectraST is that the DECOYS are >> going to be different, so you have to take that into consideration if you >> are combining SpectraST results with other search engines and have >> different sets DECOYS sequences then the result should probably not be >> combined with the NSS model on. I am working on something that will >> facilitate the combining of SpectraST results with other search engines. >> For now however, you can run iProphet on the SpectraST search results >> independently. >> >> Cheers, >> -David >> >> On Tue, Sep 26, 2017 at 2:24 PM, Adam R <[email protected]> wrote: >> >>> Thanks David for the tip! I will give MSFragger a try but unfortunately >>> I will have to wait for MTA authorization. In the meantime, would there be >>> any limitation to using a comet-generated pep.xml file using a wide-mass >>> window? Is the MASSDIFFMODE feature compatible with comet? Would there be >>> any compatibility issues when combining with SpectraST results in iProphet? >>> >>> Best, >>> >>> Adam >>> >>> On Tuesday, September 26, 2017 at 11:00:24 AM UTC-5, David Shteynberg >>> wrote: >>>> >>>> Hi Adam, >>>> >>>> Yes there is a mode in PTMProphet you can enable called MASSDIFFMODE, >>>> it will localize the mass difference like a PTM. I have tried this using >>>> MSFragger and tier-wise open mass searching using SpectraST. >>>> >>>> -David >>>> >>>> On Mon, Sep 25, 2017 at 11:09 AM, Adam R <[email protected]> wrote: >>>> >>>>> Hi David, >>>>> >>>>> Thank you for the prompt response! I will give it a try from the >>>>> command line. I also have a follow-up question to ask to this as I have >>>>> been wondering about other ways to tackle the data. >>>>> >>>>> Gygi's group published a paper in 2015 (http://www.nature.com/nbt/jou >>>>> rnal/v33/n7/abs/nbt.3267.html) about using wide mass tolerance >>>>> windows for searching spectra (+/- 500 Da windows) to identify >>>>> modifications in unassigned spectra. They went on to use the Ascore >>>>> algorithm to identify the sites of modifcation. I'm wondering whether this >>>>> would be possible to perform with the current iteration of TPP? (i.e. wide >>>>> mass tolerant search with comet followed by site analysis by PTM Prophet) >>>>> PTM Prophet's input requires the amino acid and the mass shifts for PTMs >>>>> but I'm wondering whether it could be utilized to identify "un-specified" >>>>> mods on any amino acid. >>>>> >>>>> Best, >>>>> >>>>> Adam >>>>> >>>>> On Monday, September 25, 2017 at 11:47:39 AM UTC-5, David Shteynberg >>>>> wrote: >>>>>> >>>>>> There are a couple things wrong here. Primarily there is a bug in >>>>>> current distributed version of PTMProphet that prevents it from being run >>>>>> through the web-interface. There is already a fix available, however, >>>>>> you >>>>>> will probably want to run this from the command line because of reasons >>>>>> that follow. Your command needs some adjustment. As is it will try to >>>>>> localize a different "PTM" on the amino acids you have specified for each >>>>>> set of amino acids, when what you want it to localize on any amino acid. >>>>>> You can try the following in a command terminal >>>>>> >>>>>> cd c:\TPP\data\[YOUR_DATA_DIRECTORY] >>>>>> >>>>>> PTMProphetParser MZTOL=0.2 ABCDEFGHIJKLMNOPQRSTUVXWYZ:639.3169 >>>>>> [YOUR_INPUT_PEPXML] [YOUR_OUTPUT_PEPXML] >>>>>> >>>>>> >>>>>> Thank you for reporting the issue. >>>>>> >>>>>> -David >>>>>> >>>>>> >>>>>> On Sun, Sep 24, 2017 at 11:19 AM, wicher89 <[email protected]> wrote: >>>>>> >>>>>>> Hi Everyone, >>>>>>> >>>>>>> I am analyzing peptides from cells that have been treated with a UV >>>>>>> crosslinker attached to a small molecule (ABPP method). This results in >>>>>>> mono-linked peptides. Because the UV cross-linker is not residue >>>>>>> specific, >>>>>>> I am forced to search the data in comet with a modification of 639.3118 >>>>>>> Da >>>>>>> on any amino acid other than those with fixed modifications. I am able >>>>>>> to >>>>>>> process the output files until the iProphet step, but am running into >>>>>>> command failure at PTM Prophet. Is there a maximum limit on the number >>>>>>> of >>>>>>> amino acids used at once in a single line entry for a modification? I >>>>>>> have >>>>>>> attached screenshots of the parameters used and the command failure >>>>>>> output. >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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. >>> >> >> -- > 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. 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