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.
