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

[Matthew C. <mat...@va...>]

Conference call notes:

Present: Matt, Jim, Ree?, Mark, Steffen, Eric

1) mzML 1.1.0

- Manuscript now in active preparation
+ draft available in a couple weeks

- Matt will release updated 1.1.1 of indexedmzML schema: <indexList> 
name attribute will be enumerated to "spectrum" or "chromatogram"
+ not yet done

- Matt will update the example files to reference mzML 1.1.0 but 
indexedmzML 1.1.1
+ not yet done

- Andreas will add "Replaced-by" field to the obsoleted MaRiMba term
+ done

- Matt added new terms for ABI TOF/TOF T2D file format
+ done

- How do we handle lock mass corrections? Matt will make an example
+ Steffen wants lock mass spectra to be marked so they can be segregated
+ Need an example of what lock mass spectra would look like in mzML, 
also what do corrected spectra look like (e.g. processingMethod)?
+ Steffen will start a ML thread with ideas on the topic.
+ CompassXport beta version supports mzML

- Other items?


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2) MIAPE-MS revision

- Pierre-Alain has sent out the revised MIAPE-MS draft 2.94 document to 
the list
- Everyone: Please examine MIAPE-MS 2.94 in Pierre-Alain Binz's email on 
2009-12-22 and respond with comments
- Deadline is Jan 12, after which the document will be submitted to the 
PSI document process
+ Pierre-Alain will address minor comments and send doc process

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3) TraML development

- Current version 0.9.3 is available at 
http://www.psidev.info/index.php?q=node/405
- Matt suggest changing "frag: y ion" to "product: y ion"
- But Andreas points out that the "frag" is supposed to differentiate 
search parameter from resulting
- Andreas will rephrase all the definitions for "frag: y ion" to be better
+ done

- Fredrik sent out an inclusion list example. Everyone look and comment.
- Andreas also sent out an example
+ not yet reviewed

- What do we do about specifying retention times, i.e. where to allow 
<RetentionTimeList> (see 1/14)
+ because of semantic differences between predicted/observed retention 
times (e.g. provided by public transition lists), should we move local 
retention time to transition or configuration?
+ local retention time under transition can override local retention 
time in Peptide/Compound
+ Eric will summarize the discussion to the list. Add <RetentionTime> to 
<Transition> and <Target>

- Do we try to merge <Transition> and <Target>?
+ Keep them separate for now.
+ Discussed the scope of TraML. We agreed that we would keep TraML 1.0 
limited to transitions and an additional add-on for inclusion/exclusion 
lists. Steffen proposes a future TraML 2.0 or MethodsML that tries to 
tackle a unified instrument input configuration or “methods file” format.

- Implementations?
  - Matt will implement in ProteoWizard
  + mostly done
  - Andreas will implement in OpenMS and update on-line validator
  + done
  - ISB implementation in ATAQS nearly done
  - Jim will implement as a test
  - David Cox at Sciex will test implement?
- Are we ready to update validator page?: http://www.psidev.info

Next meeting:
+ Eric is unavailable in two weeks, next meeting is in 3 weeks on 
February 9th at regular time.