Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

[Stein, S. E. Dr. <ste...@ni...>]

Congrats on a new version.....

However, I wanted to again state what I think is a defect in the standard - the inability to accept an ASCII peak list. This prevents us from using mzML it as the format for libraries or reference data.

--- 1 is different than 1.0 and different than 1.00 ....

this difference, to some, is non trivial and changes the meaning of reference data when converted to binary.

Also, the ability to see read the data is nice for those who want to do it.

I suppose it's addition will do too much damage to add to 1.2 - but I just felt that I should bring it up again as our needs have not changed.

-Steve Stein

________________________________
From: Eric Deutsch [mailto:ede...@sy...]
Sent: Tuesday, June 09, 2009 12:02 PM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

Present: Marc, Jim, Matt, Eric, Lennart, Pierre-Alain

1) mzML 1.1.0
- Released!
+ The whitespace issue in the xsd resolved before
- Allowed binarydata data types
+ Add back in 32- and 64-bit integer. Those terms should be unobsoleted. There were there
+ Add string array: null-terminated array of strings. Must have as many nulls as elements.
+ Matt will add these to the CV
+ It will be implemented somehow in ProteoWizard and OpenMS
+ Matt will added another CV type which is binarydatatype and then annotated mzArray, IntensityArray, and chargeArray with the appropriate types
- ASMS
+ There is a group that just put together a "unified" format for ion mobility mass spec. Matt and Eric met him, and we will followup
+ Also had discussion with ANiML. Being done through ASTM
- ASMS might help out with CV
+ David Sparkman may help us out.
+ Eric will update MSS WG page
+ Eric will email Juan Antonio about top page
+ Marc will double check with Andreas Römpp on units addition and then add them as is

2) TraML development
- Feedback from ASMS
- Implementations
+ ProteoWizard has some implementation. OpenMS does as well by Andreas. Jim is working on something
- cvParams vs attributes
+ Problem with attributes is lack on units specification
+ Problem with attributes is default value ambiguity in C++
+ change transition name to id of type xsd:string
+ Apply rule: any attribute that is not an id or a Ref should be switched to cvParam
+ How does mzIdentML handle b9-18^2 ? Try to do he same?
+ What about string values?
+ Matt is advocating more cvParams, Pierre-Alain as well. Jim as well.
+ Make normalizationStandard should be cvParams H-PINS
+ Eric will make another rev beased on this.

+ Meet again next week same time


________________________________
From: Eric Deutsch [mailto:ede...@sy...]
Sent: Monday, June 08, 2009 3:41 PM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: PSI-MSS WG Tuesday call reminder

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT:

http://www.timeanddate.com/worldclock/fixedtime.html?day=09&month=6&year=2009&hour=16&min=0&sec=0&p1=136

08:00 San Francisco
11:00 New York
16:00 London
17:00 Geneva

+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ USA: 1-866-314-3683
Generic international: +44 2083222500 (UK number)

access code: 297427

Agenda:

1) mzML 1.1.0
- Released!
- Allowed binarydata data types
-

2) TraML development
- Feedback from ASMS
- Implementations
- cvParams vs attributes