Re: [Psidev-ms-dev] Demultiplexing overlapped/MSX spectra

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

Hi Matt, thanks for bringing this up. I don't see an immediate best
solution, so I'll think out loud for a bit...

The schema at <spectrum>
http://www.peptideatlas.org/tmp/mzML1.1.0.html#spectrum

The CV  for identifier formats:
http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibr
ary.org%2Fobo%2FMS_1000767

One could imagine just using the plain nativeID term to just use an
arbitrary index for each spectrum.

Perhaps it might be useful to extend the vendor specific terms by adding a
demux= field, but I wonder if that would break most existing code:

controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger
scan=xsd:positiveInteger demux=xsd:positiveInteger

and it would need to be done for each vendor.

Maybe there should be a child term under spectrum representation called
"demultiplexed spectrum"
http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibr
ary.org%2Fobo%2FMS_1000525

I think I agree that the demultiplexed spectrum should refer to the
original scan in the <scan> element.

Maybe it would best to come up with a single hand-crafted example for us
to debate over.

Can you come up with a good example of what you think would work best for
ProteoWizard?

Thanks,
Eric



-----Original Message-----
From: Chambers, Matthew [mailto:mat...@gm...]
Sent: Tuesday, September 27, 2016 1:35 PM
To: Mass spectrometry standard development
<psi...@li...>
Subject: [Psidev-ms-dev] Demultiplexing overlapped/MSX spectra

I am integrating some demultiplexing algorithms into ProteoWizard that
take overlapping DIA spectra or multi-isolation-window (MSX) spectra and
expand them to multiple single-isolation-window spectra. What nativeID
should the new spectra get? This is basically the opposite of the
scan-summing problem, which we theoretically came up with a solution for,
but don't see it used much. Should each demux'd spectrum refer back to the
original spectrum in the <scan> element?

-Matt

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