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

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

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



http://www.timeanddate.com/worldclock/fixedtime.html?day=5&month=1&year=2010&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

- Manuscript now in active preparation

- Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name
attribute will be enumerated to “spectrum” or “chromatogram”

- Matt will update the example files to reference mzML 1.1.0 but indexedmzML
1.1.1

- Andreas will add “Replaced-by” field to the obsoleted MaRiMba term

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

- How do we handle lock mass corrections? Matt will make an example

- 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



----

3) TraML development

- Current version 0.9.2 is available at
http://www.psidev.info/index.php?q=node/405

- Version 0.9.3 about to be released

- Use Andreas’s suggestion to use 'isolation window target m/z', MS:1000827

- Eric will update the examples and mapping files for that.

- Eric will add term: “product interpretation rank”

- 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

- Eric made a change to the 0.9.2 schema to make all elements be a
complexType definition

- Eric will release 0.9.3 as soon as these other additions are made

- Eric is having a problem with keys and keyrefs. They’re  not being
enforced

- Eric will send the problem to Matt who will look at it

- Fredrik sent out an inclusion list example. Everyone look and comment.

- Fredrik did use the 'isolation window target m/z' term. Update mapping
file

- Andreas also sent out an example

- Address Andreas’s suggestions in his email

- Matt asks if we should use lowercase CvParam like mzIdentML? Seems like
consensus to change CvParam -> cvParam, UserParam -> userParam

- Eric will send out new version 0.9.3

- Implementations?

  - Matt will implement in ProteoWizard

  - Andreas will implement in OpenMS and update on-line validator

  - 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/index.php?q=node/304