Re: [Psidev-ms-dev] TraML format

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

Hi Alexey, I'm not certain I've fully understood your request, but here is
what I can say:

1) There is at present no distinction between direct injection and an SRM
trace. We can add terms to differentiate this if you think it is
important.

2) TraML is designed as a mechanism for sharing transition lists. It is
not designed for encoding quantitative results. When you encode in
<ValidationStatus> are the intensities relative to other fragment ions of
the same peptide ion, measured in some way. Ideally the relative
intensities should be the same when measured by direct injection or by a
full LC run. There is no functionality for encoding that a certain
transitions is suitable in tissue but not plasma, for example. These are
all potential use cases, but none of this information is encoded in any of
the formats we're trying to unify, so for the moment this is beyond our
scope.

3) To the same point, TraML is not intended to convey quantitative
measurements. We recommend mzQuantML for this.

Can you clarify: are you trying to encode quantitative results from an SRM
experiment? OR are you interested in encoding a transition list to be
share with very high level of detail on its pedigree?

Thanks,
Eric


> From: Alexey Chernobrovkin [mailto:che...@gm...]
>
> Dear All,
>
> I'm trying to fit new TraML format to our set of SRM/MRM data and I
> have several questions:
> 1. My transitions were "optimized on specified instrument", but we
> didn't use direct injection of the peptide. I can't find any MS
> ontology term which describes using MRM-measurements on biosample for
> transitions optimization.
> 2. I want to provide quantitative data with my transition, including:
> 	- peak area (integrated)
> 	- peak height (maximal intensity)
> 	- peak width
> 	- signal to noise value for the peak
> Should I provide these data in <ValidationStatus> tag using <cvParam>
> elements? In this case i have some problems with ms ontology:
> 	- there is no term "signal to noise" in MS ontology.
> 3. How (and where) can I specify and annotate the biosample in which
> measurements were carried out?
>
> Alexey Chernobrovkin
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