Hi Surendra, The warning indicates that the correct modification specifications were not written as <aminoacid_modification> tags to the <search_summary> section of the pepXML. I guess just writing the <mod_aminoacid_mass> tags in the <search_hits> might be an improvement over just dropping them, but the real solution should be to figure out why the <aminoacid_modification> tags aren't getting written.
Is there anything in the X! Tandem parameters than can be read as indicating that these modifications are possible? Usually there is. If you don't write internally consistent modifications, some tools like CPAS (on which I was working when I wrote Tandem2XML) will have difficulty consuming the resulting pepXML. I am sure Jimmy Eng or Brian Pratt (included on this message) can help you connect with people currently working on the TPP. --Brendan On Dec 10, 9:24 am, dasaris <[email protected]> wrote: > Hi There, > > I noticed an issue in Tandem2XML program. When the > program encounters a modification that is not in input parameters, it > issues an "unknown modification" warning and ignores it. However, this > often happens when people search for point mutations with X! Tandem. I > fixed the program such that it will write any unknown modifications to > the pepXML instead of ignoring them. Let me know if you are interested > in getting the fix into your source tree. > > Thanks, > Surendra -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
