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]. 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.
