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

[Eric D. <ede...@sy...>]

Hi Steffen, Andreas, Fredrik, et al. thank you for this discussion on
Steffen's proposal. The history here is that we set out to create a format
for transitions only. The primary use cases all were for SRM experiments.
This has not yet been clearly written in the spec doc as you noted. But
then it was suggested that we could easily add inclusion/exclusion lists
as well. It seemed unclear to me that there would be much interest in
sharing inclusion lists (in my mind, transition lists have great reuse
potential, but inclusion lists far less so), but it seemed reasonable to
add this on to permit certain additional use cases as there was no
alternative and this would be the closest similar format. However, I, too,
am hesitant to complicate the <transition> design (and hinder validation,
e.g. how do you prevent transitions with no Q3 value?) by trying to fit
this additional potential use case into our current design.

Steffen, thank you for writing the use case section. I will insert this
into the spec doc and perhaps expand on it a bit.

If there are addition comments, please do speak up. Let's also entertain
this idea bit more on Tuesday's phone conference.

Thanks,
Eric


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: Wednesday, January 13, 2010 5:52 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Is a <transition> a <target> with an
> additional <product> ?
>
> 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
>
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>
>
> -----------------------------------------------------------------------
> -------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev