Re: [Psidev-ms-dev] Better coverage for metabolomics and GC/MS in particular

[Steffen N. <sne...@ip...>]

Hi Nils and others, 

there are three aspects that immediately come to mind, 
and I am keeping a sourceforge tracker[1] for COSMOS 
(which I started only today, so very little content yet).

1) Add missing CV terms, which we already started 
   about a year ago with IIRC stuff like 
   MS:1002040 / inlet temperature. Also, we'd need to 
   complete the coverage of instruments in the CV.

   Most of these will be fairly trivial.

2) Add the GCxGC (and also cover LCxLC) we discussed a few weeks ago
   to the examples and the specification document, so that not only 
   maltcms can deal with it ;-)

3a) Improve support for software converters to mzML 
    for GC instruments, and document that. I heard 
    that LECO has mzML export somehow, but I haven't seen it 
    anywhere yet. Some companies (Waters GCT Premier, 
    Bruker APCI micrOTOF) can use the "normal" proteowizard converters.

    Again, that should be documented somewhere. 
    Maybe complete "Current and future support for mzML:"
    on http://www.psidev.info/mzml ?

3b) Improve support for software readers/data processing.
    So maltcms we can tick off already, xcms is fine as well,
    mzmine2 should be able to process the data. 
    I'd like to pursuade projects like pyMS [2] to 
    adopt stuff like pymzML [3] and so on. 

Really, what I'd like to have in the end is that 
Metabolomics GC/MS data is archived as mzML, 
rather than netCDF today. People start to use
GC/[EI|APCI]-QTOF-MS or other interesting technologies,
and I'd love to have mzML being a possible unified format.

Yours,
Steffen

[1] https://sourceforge.net/p/cosmos-fp7/tickets/    
[2] https://code.google.com/p/pyms/ 
[3] https://github.com/pymzml/pymzML

On Fri, 2012-11-16 at 12:16 +0100, Nils Hoffmann wrote:
> Sorry for the previous post in german, I was too fast in replying and
> hit 'the other' address :-).
> I would like to also congratulate Steffen on this project and I am looking
> forward to seeing his recommendations.
> 
> Nils
> 
> Am 16.11.2012 11:39, schrieb Nils Hoffmann:
> > Hi Steffen,
> > herzlichen Glückwunsch, das klingt nach sehr viel Arbeit im Vorfeld.
> > Welchen Aspekt von GC-MS Daten willst Du denn in mzML besser abdecken?
> >
> >
> > Gruß,
> > Nils
> > Am 16.11.2012 07:57, schrieb Steffen Neumann:
> >> Good morning,
> >>
> >> you may have seen my name on this list before,
> >> but recently we at the IPB received a new hat:
> >> namely the "COSMOS WP2 Standards Development" - hat,
> >> see also http://www.cosmos-fp7.eu/wp2
> >>
> >> One of the aims is to improve the handling of GC/MS data
> >> in mzML, so expect to see a few requests to add new instruments 
> >> and GC-specific terms to the psi-ms.obo
> >>
> >> We'll also later try to contribute to other PSI standards,
> >> to enable their adoption in the metabolomics community,
> >> stay tuned.
> >>
> >> I am looking forward to work with the PSI,
> >> and get metabolomics where proteomics already is
> >> in many aspects.
> >>
> >> Yours,
> >> Steffen
> >>
> >
> 
> 

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409