Hi Luis,
how are you doing? I hope very well!
When is TPP 5.0 coming? I would like to include it into MASSyPup64 to
provide it "ready to use" for interested users.
On the other side, I have some trouble to convert .prot.xml TPP outcome
to .mzid -> it is not accepted by ProteomeXChange. Is there a trick?
Best Regards, Robert
On 27/07/16 17:00, Luis Mendoza wrote:
This has been fixed in the new schema (pepXML_V120.xsd), which is
already on our code repository, and scheduled to be released with TPP
5.0 soon.
Cheers,
--Luis
On Thu, Mar 3, 2016 at 9:37 AM, David Shteynberg
<[email protected]
<mailto:[email protected]>> wrote:
Hello Mal,
Your point seems valid to me. Getting the an old demo file to
validate against the schema shouldn't warrant requiring this
information to be present multiple times in the file. We will
correct this problem for a future schema version.
Thanks for your detailed report!
-David
On Thu, Mar 3, 2016 at 3:28 AM, Mal Ross <[email protected]
<mailto:[email protected]>> wrote:
Hi there,
I was just looking back through the history of the PepXML
format
<https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/schema/>
and
noticed that the latest commit shown for pepXML_v112.xsd
mentions the removal of the search_engine attribute from the
msms_run_summary element:
https://sourceforge.net/p/sashimi/code/4028/
However, in pepXML_v118.xsd, I see that this attribute has
returned in a commit that's aimed at getting a demo2009 file
to validate: https://sourceforge.net/p/sashimi/code/6143/
Does that mean the attribute should never have been removed in
the first place? It actually strikes me that it was /correct/
to remove it and that the subsequent /reintroduction/ is
misguided, as child search_summary elements have their own
search_engine attribute anyway. However, any guidance on this
would be appreciated.
Thanks,
Mal.
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