[Psidev-pi-dev] storing intermediate results in mzML

[Richard S. <r.a...@ru...>]

My email ended up only in ms-dev, so trying to repost here to.



Dear all,

Thank you for your comments. A question from my side, is the phone 
conference scheduled for this afternoon open? As I'm on the agenda I 
would like to join if possible.


Matthew Chambers wrote:

> > I'm not sure what this would look like. We certainly didn't have 3d 
> > chromatograms in mind, but perhaps they can be accommodated. Would that 
> > be a chromatogram with three axes (data arrays): time, m/z, and 
> > intensity? Is this akin to the "psuedo-2d-gel" view?
>   
The mass chromatogram would indeed consist of time, m/z and intensity. 
The m/z data coming from the profile spectrum data. If you plot the mass 
chromatogram it will look a bit like a bell. I'm not quite sure what you 
mean with the pseudo-2d-gel view, but as I understand it, this is a 2d 
view of all the mass chromatograms found in for example a LC/MS profile. 
In the definition of the chromatogram block some semantics should be 
worked out in order to let the parser figure out what is stored there.

I would suggest something as following (a mass chromatogram spanning 9 
scans, sorry for the verbosity of it all). For the centroid data the 
original structure would hold with the addition of the cvParam MS:1000127:

<chromatogram id="0" index="0" defaultArrayLength="9">
   <cvParam cvRef="MS" accession="MS:1000627" name="selected ion current 
chromatogram" value="" />
   <cvParam cvRef="MS" accession="MS:1000128" name="profile mass 
spectrum" value="" />
  
   <binaryDataArrayList count="19">
      <binaryDataArray encodedLength="36">
         <cvParam cvRef="MS" accession="MS:1000519" name="32-bit 
integer" value="" />
         <cvParam cvRef="MS" accession="MS:1000576" name="no 
compression" value="" />
         <cvParam cvRef="MS" accession="MS:1000595" name="time array" 
value="" />
         <binary>.......</binary>
      </binaryDataArray>
      // scan 0
      <binaryDataArray encodedLength="72">
         <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" 
value="" />
         <cvParam cvRef="MS" accession="MS:1000576" name="no 
compression" value="" />
         <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" 
value="" />
         <binary>.......</binary>
      </binaryDataArray>
      <binaryDataArray encodedLength="72">
         <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" 
value="" />
         <cvParam cvRef="MS" accession="MS:1000576" name="no 
compression" value="" />
         <cvParam cvRef="MS" accession="MS:1000515" name="intensity 
array" value="" />
         <binary>.......</binary>
      </binaryDataArray>
      // scan 1
      ...
   </binaryDataArrayList>
</chromatogram>

> > Yes, I think a background ion chromatogram is reasonable. But there may 
> > be some semantics to work out: is there a distinction between 
> > "background ions" and "noise"? I know there are different kinds of noise 
> > to think about...
>   
There is a distinction between noise and background ions. The definition 
for a background ion should according to me in LC/MS be a compound which 
is continuously eluting from the LC/GC or continuously being injected 
into the MS. A famous example of this would be PEGs dissolving from the 
plastic tubing used to transport the sample from the LC to the MS. So 
background ions are real (usable) compounds, while noise are artefacts 
from the measurement technique used not describing a real compound. 
Isomers forming a peak on top of the elution pattern of a background ion 
should probably be removed.

If this definition is maintained I think the addition to the CV that I 
proposed still holds, but I could be wrong and more is necessary? 
Probably single spectra (no separation up front) would suffer a bit, 
although then we're not really talking about a chromatogram right?

 name: backgroundion chromatogram
 is_a: chromatogram type (MS:1000626)
 definition: chromatogram created by creating an array of a ubiquitously present mass.


David Creasy wrote:

> > We're still alive (I think!), but I don't think we have what you want:
> > http://psidev.info/index.php?q=node/319
>   
My _very_ quick overview would make me agree. How would we continue from 
here?



Cheers,
Richard

-- 
Drs. ing. RA Scheltema    Groningen Bioinformatics Centre
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