Thanks David for the reply and for the future work! I will see how the comet results turn out and report anything (hopefully) useful.
Best, Adam 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] <javascript:>> > 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/journal/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] <javascript:>. >> To post to this group, send email to [email protected] >> <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 [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.
