Hi Brendan, Currently, Tandem2XML scans the “potential modifications” tags of tandem results file and writes them to the modification summary in the pepXML. Point mutations would not be listed in “potential modifications” tags of tandem results file. Only way you can find out about them is to look for “point mutations” tag in the tandem XML. If that tag is set to “yes”, then you have to pre-scan all peptide- spectral matches (PSMs), build a table of point mutations seen in the entire file, and write them to modification summary.
Another clean way of doing the same is to ignore the “potential modifications” tag altogether. Pre-scan all PSMs for mods, and build a table of seen mods, and write them to the modification summary. This would option would work regardless of whether tandem is configured to find mods or mutations. Both these options require a redesign of the Tandem2XML source. Meanwhile, I put in a stop gap fix that would write unknown mods to pepXML instead of ignoring them. To me, ignoring them altogether is a bigger problem than leaving them out of modification summary. Sure, it produces inconsistent pepXMLs for programs that look at the modification summary, but my feeling is that not a lot of programs look at that summary. Thanks, Surendra On Dec 11, 10:38 am, Brendan <[email protected]> wrote: > 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.
