Re: [Psidev-ms-dev] indexedmzML: scanNumber / acquisition number

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

Ugh. I don't think there should be any reference to acquisitions in the 
index; there is no 1:1 mapping and mapping to the first of the 
acquisitions is counter-intuitive. The scanNumber attribute in the index 
offsets should be replaced by the 0-based index (now that there is an 
index attribute on the spectrum) and if you want to refer to a Thermo 
spectrum by its original scan number, that will somehow have to be 
parsed from the spectrum id attribute or you can generate the 
index->scan mapping when reading and/or generating the file index.

-Matt


Kessner, Darren E. wrote:
>
> Hi all,
>
>  
>
> Please correct me if I'm wrong, but I believe the consensus now is to 
> encode the Thermo scanNumber as the (first) acquisition number:
>
>  
>
>     <spectrum id="S17" index="0" msLevel="1" arrayLength="1313">
>
>         ...
>         <spectrumDescription>
>
>             <acquisitionList count="1">
>
>                 <acquisition number="17" spectrumRef="?" 
> sourceFileRef="?"/>
>
>             </acquisitionList>
>
>             ...
>
>         </spectrumDescription>
>
>         ...
>
>     </spectrum>
>
>  
>
> However, when the mzML is indexed, we still have <offset> entries with 
> attribute 'scanNumber':
>
>  
>
>     <index>
>
>         <offset id="S17" scanNumber="17">4826</offset>
>
>     </index>
>
>  
>
> Shall we make this:
>
>         <offset id="S17" acquisitionNumber="17">4826</offset>
>
> and assume it refers to the *first* acquisition number in the 
> <acquisitionList> ?
>
>  
>
> The use case is the same -- for efficient random access by Thermo 
> scanNumber we need this in the <index>.
>
>  
>
> Previously I had also proposed including the 0-based index, which was 
> deemed unnecessary (and I agree), but someone may want it now for 
> consistency and/or validation?
>
>         <offset id="S17" index="0" acquisitionNumber="17">4826</offset>
>
>  
>
>  
>
> 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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