Hi Josh,
Thanks for the bug report and patch.  It will be included in our next
release.

As for the extra "<kappa>" tags you get, how are you running the command?
I have not been able to reproduce it with various configurations.  For what
it's worth, writeTraditional() is a template defined in Parser/Tag.cpp .
I'd be glad to take a further look at it if you can send me the relevant
files that expose this behavior.

One thing I did notice while trying to repro this, is that Mascot2XML will
sometimes pull the wrong protein description when one protein accession is
a substring of another and the longer version is found earlier in the
protein database.  For example, the description for "IPI1234" might be
filled in with the one for "DECOY_IPI1234" if that decoy entry comes first
in the file.

It also seems that Mascot itself does not fully report all of the possible
proteins that a given peptide maps to (at least with a sample file I had).

For these reasons, I would strongly suggest running RefreshParser after the
conversion, and using the resulting file for downstream analysis.

Cheers,
--Luis


On Wed, Sep 28, 2016 at 5:09 PM, Josh Eckels <jeck...@labkey.com> wrote:

> I'm working with some users who are generating a malformed pepXML file by
> using Mascot2XML when the protein description includes special XML
> characters, like < and >. The output pepXML file includes this text:
>
> ...
> <alternative_protein protein="tr|A0N5G5|A0N5G5_HUMAN"
> protein_descr="Rheumatoid factor D5 light chain (Fragment) OS=Homo sapiens
> GN=V<kappa>3 PE=2 SV=1" num_tol_term="2" peptide_prev_aa="R"
> peptide_next_aa="A"/>
> <kappa>
> <kappa>
> <search_score name="ionscore" value="46.68"/>
> ...
>
> Note the "<kappa>" that's included, unencoded in the value of
> the protein_descr attribute.
>
> I'm attaching a patch, which uses the same encoding approach that's being
> used for the primary protein identification as of 2010 with revision 4877.
>
> However, I'm also worried about the unclosed <kappa> tags immediately
> afterwards. I assume that's coming from the modtags code a little later in
> that same function. However, after a little poking around, I've been unable
> to find the implementation of writeTraditional(). Anyone have ideas on what
> might be going wrong here?
>
> Thanks,
> Josh
>
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