Re: [Psidev-ms-dev] multiple precursor reporting

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

I also agree with these sentiments. Although the primary intended use
case for mzML is a faithful, open representation of what was produced by
the instrument control software, in practice mzML should be a convenient
vehicle for feeding data into search engines. If mzML does not capture
the kind of data and information that users want to feed into their
search engine, then those people will continue to use mzXML for this
purpose and I don't think we want to encourage that.

I could easily see a workflow where one could use a "converter" program
to convert 123.RAW to 123.mzML without any conversion flags on and then
also convert 123.RAW to 123_proc.mzML, wherein the spectra have been
centroided, deisotoped, more accurate precursor masses calculated, etc.
with proper documentation of these modifications in the header. It would
then be 123_proc.mzML that was fed into the search engine and used for
all downstream analysis. If we don't facilitate something like this, we
won't have solved the multiple format problem.

Eric


> From: psi...@li...
[mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Matthew Chambers
> Sent: Monday, November 26, 2007 2:28 PM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] multiple precursor reporting
>=20
> Indeed, we must be careful where we draw the line.  We should keep in
> mind that centroiding, charge deconvolution, and deisotoping are
> certainly kinds of peak processing and they are already integrated
into
> all 3 Mass Spec XML formats.
>=20
> -Matt
>=20
> Darren Kessner wrote:
> >
> >
> > In regard to mzML, I expect that this sort of preprocessing will
> > become part of the normal data pipeline, so I hope that a hard line
is
> > not drawn between acquisition data and analysis in the definition of
> > the format.
> >
> >
> > Darren
> >
>=20
>=20
>
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