Re: [Psidev-ms-dev] How to encode MS3 in TraML?

[Steffen N. <sne...@ip...>]

On Mon, 2011-03-14 at 11:55 -0700, Eric Deutsch wrote:
> QTRAP 5500. The group discussed this on a call some time ago, and it
> seemed like the simplest way to implement this would be via multiple
> <Product> elements. 

Why not multiple <Precursor> ? Or, even more adventurous, 
nested <Precursor> ?  

> A) Rely on tag order to denote the various levels of fragmentation:
Probably the weakest option, since you can't rely 
on the ordering in XML through various transformations,
such as database persisting etc.

> B) Explicity provide an ordering via order attribute:
Semantically vague, the additional information should 
more closely resemble the MS experiment.

> C) Explicitly state an MS level, which accomplishes the same thing,
> but also provides more information:
Makes sense. 

Now that we're including MSn, we should make sure it is treated 
as a first-class citizen, and that the current MS2 handling 
is just a subset of MSn:

* Can we encode different collision energies in MS2/MS3 ?
  Currently, CE is encoded in <Configuration> of which 
  there can be only one per <Target>. 

  - Include MSn settings in the <Configuration> ?

  - Should we allow multiple <Configuration>, 
    and require referencing from the <Precursor> ?

  - Allow additional <cvParam> which carry a subset of what 
    is otherwise kept in <Configuration> ? Better not.
  
* Other points ?

Yours,
Steffen


-- 
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