Re: [Psidev-ms-dev] mzML's binary arrays

[Slotta, D. (NIH/NLM/N. [E] <sl...@nc...>]

A translation for those of you lucky enough not have an office mate whose native language is German:

"Hey,

If I am reading this right, the FeatureFinder will soon spit out mzML as well as FeatureXML?" 

Greetings,
Steffen"


Douglas

> -----Original Message-----
> From: sneumann [mailto:sne...@ip...]
> Sent: Wednesday, June 25, 2008 6:23 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] mzML's binary arrays
> 
> Moin!
> 
> Sehe ich das richtig, dass der FeatureFinder demnächst neben FeatureXML
> auch mzML ausspuckt ?
> 
> Gruss,
> Steffen
> 
> On Mi, 2008-06-25 at 09:16 +0200, Marc Sturm wrote:
> > Hi Eric,
> >
> > i agree that less custom encoding is desirable to make files
> > exchangable between different tools. However in this case i would go
> > both ways, depending on the significance of the term.
> >
> > (1)
> > I use these arrays to store debug information of an algorithm and add
> > quite a few arrays, depending on the charge states i look at:
> >
> > pattern_score_1
> > pattern_score_2
> > pattern_score_... (one per charge)
> > intensity_score
> > local_maximum
> > trace_score
> >
> > Putting the name in the userParam is not a good idea because it makes
> > these arrays unusable for other tools - too custom in my opinion.
> > Adding a CV term for each such debug variable would however be too
> much.
> > So i think the intermediate way is just right:
> > Terms which are not generally usable should be put to a 'named custom
> > array'. This would correpond to an optional XML attribute 'name' for
> > the 'binaryDataArray' tag.
> > But we have to state clearly in the documentation that for more
> > general terms, a CV entry should be added.
> >
> > (2)
> > After peak picking we store much more information than the position
> > and intensity. The arrays there are:
> >
> > SignalToNoise
> > fwhm
> > leftWidth
> > rightWidth
> > maximumIntensity
> > peakShape
> > rValue
> >
> > 'SignalToNoise' is alread a CV term. 'fwhm' would be a good candidate
> > for a CV term as well.
> > The rest is more algorihtm-dependent and no general concept which is
> > why we could simply store them in a 'named custom array'.
> >
> > What do you think?
> >
> > Best,
> > Marc
> >
> > > Hi Marc, I think we would be better off creating CV terms for all
> > > the kinds of arrays people want to encode. So I'm much rather get a
> > > request that someone's software wants to write out "full width at
> half maximum"
> > > and create a term, furnish an accession number, and thereby
> publicly
> > > let all writer and reader authors know that this is a legal entity
> > > that could occur. No schema change is necessary.
> > >
> > > I find this preferable to having a vague slot that could be filled
> > > with
> > >
> > > full width at half maximum
> > > full width at half max
> > > FWHM
> > >
> > > in an uncontrolled and variable way.
> > >
> > > This is our general aim for mzML. We would like to steer away from
> > > custom ways of encoding data as much as possible.
> > >
> > > Does that seem reasonable?
> > >
> > > Would you like "full width at half maximum" to be added to the CV?
> >
> >
> >
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> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
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