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

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

On Wed, 2010-01-13 at 13:12 +0100, Andreas Bertsch wrote:
> I agree with Fredrik. The costs for the simplifications are too high.
Yes, it's not for free :-(

> Separating the targets and transitions seems reasonable to me, because
> these are to very different things.
Are they ? 

Analytically yes, because you program the MS machine 
in different ways, either (auto-)MS/MS or SRM.

Conceptionally no, because if I have observed a pair 
of precursor/product ions and use that as a hint that 
the predicted interpretation is true, no matter whether 
you have measured that by SRM or a normal QQQ 
or QqTOF tandemMS experiment. Granted, only the <precursor> 
information will not be enough for a usable <interpretation>.

On the other hand, to analyse a normal tandemMS experiment,
you could even specify multiple <product>s for one precursor,
which you require for a sufficiently confident peptideRef="ABC".
(If I saw that correctly from the traML schema, the current approach
 is to create multiple <transition> to hold multiple <product>s)

Again, I think I can be persuaded/convinced if there 
is a definition of use case(s) for traML, and my ideas 
fall well outside of it. Has anyone start that already ?

> 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.
And that even allows the mapping file to distinguish between 
a retention time inside a <transition> vs. a retention time 
in a <target>. But that should not be the main point.

Yours,
Steffen

-- 
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