Hi Ali,
Thanks for sending the parameters section of your X! Tandem results.
I see the problem now. Your parameters include:
<note type="input" label="refine, modification mass">57....@c</note>
<note type="input" label="residue, modification mass">57.021...@c</
note>
As it turns out, Tandem2XML does not support the "refine, modification
mass" parameter, because pepXML provides no mechanism for expressing
differently applied static modifications. In pepXML static
modifications apply to the entire pepXML file.
In your case, however, the refine parameter is really just the same
value with less precision. I can't remember if you need to specify
the @C modification change, if it has not changed to have apply to
refinement, or if it only needs to be used as an override. If you do
need it then you should make sure it is identical character for
character with the "residue, modification mass".
--Brendan
On Aug 28, 4:57 pm, Brendan <brend...@proteinms.net> wrote:
> Hi Ali,
> Yes, it will affect the output. It means that the converter does not
> understand how the modification 57.021 ended up on C, based on the
> parameters X! Tandem reports at the end of your file. Because,
> Tandem2XML has not reported a corresponding <aminoacid_modification>
> tag in the <msms_run_summary>, it will drop this modification, and not
> report it.
>
> X! Tandem really has a lot of ways to specify modifications in its
> parameters. When I wrote Tandem2XML, I covered as many as I could,
> but also put this warning in place to help catch those that I hadn't
> anticipated. It has generated several reports that improved
> Tandem2XML's handling of these modifications, but it sounds like you
> have discovered a new one. Though, I would expect something like
> carbamidomethylated cysteine to be just a normal static modification.
>
> If you attach the end of your .tandem file, where all the paramters
> are listed, I'll have a look, but I am no longer putting much work
> into Tandem2XML. I may, however, be able to explain to you a work-
> around, or point someone else in the right direction for a fix.
>
> --Brendan
>
> On Aug 25, 3:26 am, Ali <a.alsha...@googlemail.com> wrote:
>
> > Hi
>
> > I've converted my .tandem files to .pep.xml successfully. However,
> > for some of the files I get this warning message:
>
> > WARNING: Unknown modification 'C' (57.021) for scan 56
>
> > Can anyone explain this warning for me please. Does it effect the
> > output.
>
> > Regards
>
> > Ali
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