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] > <javascript:>> 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] <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.
