Re: [Psidev-ms-dev] <scan> nativeID

[Matthew C. <mat...@va...>]

Agreed about the consistency between metadata available in the spectrum 
element and the offset elements (though I still say the offset element 
needs to be specific to the type of element it is referencing, e.g. 
"spectrum_offset", so that we can index other things if we start to 
support them, e.g. chromatograms).

NativeID is a big new concept though (as far as I know it hasn't been 
discussed before, but there was a lot mzML work before I started paying 
attention, so maybe it has come up), which brings up its own issues. Do 
vendors get to decide what the nativeID formats look like? Does it go 
through some approval process like the CV terms? Does it go into the CV 
in some way? Do non-native formats get their own nativeIDs, e.g. 
DTA/MGF/mzXML/mzData? I am excited about the concept and what it means 
for not having to mess much with arbitrary string ids, where the only 
presentation is linear and unintuitive, and the id formats are 
completely non-standard and user/writer-defined.

-Matt


Kessner, Darren E. wrote:
>
> Hi all,
>
>  
>
> To pick up the discussion regarding <index> with nativeID, since we have:
>
>   <offset id="S19" nativeID="19">1234</offset>
>
>  
>
> It would also be convenient, and consistent, to have nativeID in <scan>:
>
>   <spectrum index=0 id="S19" nativeID="19">
>
>   ...
>
>   </spectrum>
>
>  
>
> In general, whatever information is in the <index> entry should be 
> easily available in the actual <spectrum> element.  It makes 
> generating the <index> a lot simpler for writers, and allows easier 
> validation of the <spectrum> for readers.
>
>  
>
>  
>
> Darren
>
>  
>
>  
>
>  
>
> Darren Kessner
>
> Scientific Programmer
>
> Dar...@cs... <mailto:Dar...@cs...>
>
> 310-423-9538
>
>  
>
> Spielberg Family Center for Applied Proteomics
>
> Cedars-Sinai Medical Center
>
> http://www.sfcap.cshs.org/
>
>  
>
>  
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