psidev-ms-dev

[Psidev-ms-dev] FW: 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=16&month=2&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 undergoing final editing

- 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

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

- Other items?



----

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 0.9.3 is available at
http://www.psidev.info/index.php?q=node/405

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

- Andreas also sent out an example

- Need to finish writing the spec doc and submit to doc proc

- 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



----

4) PSI workshop in Seoul preparation



----

5) Working with ASMS on controlled vocabulary

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

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

Notes  from today’s call:



Present: Richard, Andreas, Steffen, Eric, Pierre-Alain, Jim



Agenda:

1) mzML 1.1.0

- Manuscript undergoing final editing

+ Final draft almost ready

- 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

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

+ Steffen has sent out new suggested CV term for “calibration spectrum” 1/19

+ The place in the schema and mapping file is already there directly under
spectrum element

+ Eric will add this to the CV, hearing no dissent

+ We should make the calibrants separate terms rather than in the value
attribute

+ Bruker: Lithium fromiate;

- Other items?



----

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 received only one comment

+ The changes have been made and other formatting changes made

+ Pierre-Alain will submit the document to the doc proc early next week

+ We should send the submitted document to all of the journal editors as a
courtesy

+ In the cover letter, suggest some editors as official reviewers

+ Advertise the official web site of the MIAPE-MS draft for everyone to
review



----

3) TraML development

- Current version 0.9.3 is available at
http://www.psidev.info/index.php?q=node/405

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

- Andreas also sent out an example

- Need to finish writing the spec doc and submit to doc proc

+ Eric will update schema to 0.9.4 with previously-discussed updates to
<RetentionTime>

+ Eric will update the spec document with contributions from Steffen, etc.

+ We will also need a few more example files

+ Andreas says he is up to date at 0.9.3

+ Jim has an implementation but just will need to update to 0.9.4

- 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



----

4) PSI workshop in Seoul preparation

+ Jim is hoping to be there

+ Henning and JuanAn will be there

+ Andy Jones will be giving MS-WG activities summary?



----

5) Working with ASMS on controlled vocabulary

+ David Sparkman and others related to ASMS will contribute to our CV as the
single standard CV

+ Eric is coordinating with them

+ Eric will update this email list with activities and non-trivial changes

+ Next call in two weeks, March 2







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Tuesday, February 16, 2010 12:40 AM
*To:* Mass spectrometry standard development; Mark Christiansen
*Cc:* ede...@sy...
*Subject:* FW: PSI-MSS WG 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=16&month=2&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 undergoing final editing

- 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

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

- Other items?



----

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 0.9.3 is available at
http://www.psidev.info/index.php?q=node/405

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

- Andreas also sent out an example

- Need to finish writing the spec doc and submit to doc proc

- 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



----

4) PSI workshop in Seoul preparation



----

5) Working with ASMS on controlled vocabulary