At least add:
ProteinPilot
ProteinLynx
Spectrum Mill
greylag
Phenyx
Proteios
Instead of looking at just which engines are compatible with TPP or can
directly output pepXML, I prefer that it supports any engine whose
output is or can be converted to pepXML (and not necessarily with just
the Analysis2XML converters). A little bird told me about a ProteinPilot
group2pepXML converter that can't be redistributed by its creators and
ABI refuses to do so even though they've had the code for about a year.
I know that Spectrum Mill and Phenyx have pepXML output as well.
Our group doesn't much care about validation errors due to an incomplete
schema enumeration, but having it in there would be nice.
-Matt
On 6/24/2010 1:19 PM, Natalie Tasman wrote:
Hi Nathan,
The search engines in pepXML are those which have been specifically
tested with the TPP. Regarding Matt's suggestion: as far as I
understand, the PSI groups are moving towards a new analysis standard:
http://psidev.info/index.php?q=node/319.
I haven't worked with that standard or followed those discussions
closely, but it might make sense to put effort into this new direction
rather than trying to extend pepXML towards a universal format.
On the other hand, if there are search engines which are compatible
with the TPP (at least, output pepXML) and are not yet in the schema,
we should definitely include those.
-Natalie
On Thu, Jun 24, 2010 at 10:01 AM, Matthew Chambers
<[email protected]> wrote:
Everything in this list would be good. Some of it isn't shotgun-capable, but
that doesn't seem very damaging:
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MS&termId=MS:1001456
-Matt
On 6/24/2010 11:53 AM, Jesse J wrote:
Out of curiosity, what search engines did you have in mind?
On Jun 24, 9:41 am, Nathan Edwards<[email protected]> wrote:
The wiki says to send this request to the spctools-dev mailing list,
but I can't find out where this list is, or how to send to it.
I'd like to request the addition of a (few) search engine names to the
pepXML search_summary entity, search_engine attribute enumeration.
How do I go about this?
Thanks,
- n
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