Re: [Psidev-ms-dev] Update from the PSI meeting

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

Hi Matt, the examples we need are mainly the off-the-beaten track things. So, a standard LTQ run we've got covered.  Here's some of what we need:

- Workin examples that include compressed spectra
- Get an example 4700 file. How to encode the sourceFile for that?
- MS^E example (I think Rune sent one out. Is it great?)
- We need to develop a good MALDI example file with spot id refs
- We need to develop a good example of a file created from individual dtas including examples to multiple possible charge states
- We need to develop a good example of a file that contains summed scans and acquisitionList
- Create an example of encoding a transient in an mzML file
- Get example than includes both PDA and MSn spectra in one file

As far as the Excel sheets, Luisa is preparing Excel sheets for each vendor with:

Accession     Model Name      Model Definition

To send to each vendor for updating/filling in so that by June 1, we have a pretty decent encoding of the current instruments in the CV.

Thanks!
Eric



> From: psi...@li... [mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Matt Chambers
> Sent: Monday, April 28, 2008 6:33 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Update from the PSI meeting
> 
> Hi Eric,
> 
> When you say you want example files, do you want the native file(s), the
> converted file, or both? Or do you mean a manually constructed example?
> I can probably get permission to release to the public some native files
> for some blank or QC runs from several different Thermo instruments
> (LTQ, LTQ/Orbitrap, Quantum). The corresponding output from pwiz's
> msconvert is trivial from that point.
> 
> What are the Excel sheets going to the vendors supposed to be for?
> 
> -Matt
> 
> 
> Eric Deutsch wrote:
> >
> > Hi everyone, we had a productive track at the PSI spring meeting. The
> > highlights are:
> >
> >
> >
> > - All suggested and needed schema revisions were completed and schema
> > version 0.99.9 is available
> >
> > - Most documentation updates were written. Revised full spec doc and
> > html doc still to be released.
> >
> > - MIAPE-MS example document almost completed
> >
> > - ASMS poster features planned
> >
> > - Journal article plans discussed
> >
> > - Some CV updates and future update procedure planned. Still much to do
> >
> > - Additional example documents are needed
> >
> > - Web site updated with completed work
> >
> >
> >
> > Many thanks to those who did the work at the workshop: Lennart Martens
> > (EBI), Pierre-Alain Binz (SIB), Darren Kessner (CSHS), Jim Shofstahl
> > (Thermo Fisher), Jari Häkkinen (Lund), Luisa Montecchi-Palazzi (EBI),
> > Randy Julian (Indigo), Lars Nilse (Manchester), Benito Cañas (Madrid),
> > Lola Gutierrez (Madrid), Matt Chambers (Vanderbilt), Alberto Medina
> > (Madrid)
> >
> >
> >
> > Moving forward, we have an aggressive schedule to release mzML 1.0.0
> > one month from now. Your participation is needed!
> >
> >
> >
> > We will have weekly teleconferences for the next month to try to keep
> > the focus strong. The next teleconference will be this Tuesday at 9am
> > PDT at the usual place.
> >
> >
> >
> > We have the following list of action items set at the end of the
> meeting:
> >
> >
> >
> > - Eric will finish documentation items (incl reviewer reply)
> >
> > - Pierre-Alain will finish MIAPE-MS example
> >
> > - Eric will do the CV to do items
> >
> > - Lennart will get validator finished and working
> >
> > - Eric will put together poster with various assistance
> >
> > - Lennart will write draft of manuscript
> >
> > - Darren and Matt and Jim will work on example files
> >
> > - Luisa will create the Excel sheets, one for each vendor. Eric will
> > send. Luisa will reintegrate.
> >
> >
> >
> > If you have an interest in mzML, we need your help to get it finished.
> > One of the important things we still need is more example files. If
> > you are willing to create from example files, especially by parts of
> > the schema that have not been well tested, please help. Create an
> > example file and post it. Or contact me for ideas.
> >
> >
> >
> > Thank you!
> >
> > Eric
> >
> >
> >
> >
> >
> >
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save $100.
> Use priority code J8TL2D2.
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/jav
> aone
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev