Re: [Psidev-ms-dev] Is a <transition> a <target> with an additional <product> ?

[Andreas B. <be...@in...>]

Hi Steffen,

I agree with Fredrik. The costs for the simplifications are too high. Separating the targets and transitions seems reasonable to me, because these are to very different things. The subelements are reused for both of the lists, which is I think a good trade-off between a light-weight schema and straight-forward structure.

Cheers,
A.

> I think your suggestion is fine and should be working. 
> InterpretationList/Interpretation, now part of  Transition, would be 
> explaining different things for included ions and transitions, though.
> 
> Even if such a change would simplify the XML schema which is good, I am 
> afraid that it would make reading of the documents a bit harder - you 
> would still like to distinguish between include targets and transitions, 
> I believe.  So in the end the current representation with separate 
> transition and target elements seems preferable to me. Or are there any 
> other practical advantages with merging of the two? Note that targets in 
> the include list can already be annotated with peptide information - 
> actually they have to be, in order to have a retention time.
>> 
>> maybe this suggestion drowned in the mail traffic 
>> that had accumulated over the holidays, 
>> so I'll bring this up again. 
>> 
>> The suggestion is to merge <transition> and <target>
>> into a single concept <target>, where the <product> is optional.
>> 
>> Comments ?
>>> this might be a bit provocative, but why are <transition> 
>>> and <target> separated ? 
>>> 
>>> Why not rename <transition> to <target>,
>>> and make the <product> optional ? This comes from 
>>> somebody who thinks of an MRM experiment 
>>> as a "degraded" tandemMS measurement (no offense meant).
>>> 
>>> If you run tandemMS on peptides, you might still 
>>> want to annotate the <TargetIncludeList> with 
>>> peptides etc, just as now the <transition>s.
>>> 
>>> To get rid of the multiple toplevel <*List>
>>> one could have a <TargetList role="include|exclude">,
>>> and the <TargetList> could have maxOccurs=2,
>>> but that could make life more difficult 
>>> for the semantic validators.

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