[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:



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 has been reviewed and the comments addressed and resubmitted.

- The editors have come back and asked for the inclusion of a “tangible
example of an application" and then it will be acceptable for publication.
Response in progress.

- Richard suggests a jzmzml as an application

- Matt suggests quantification, wiff files, spectrum annotation

- Eric will write this and send back in

- Matt has released and posted the updated 1.1.1 version of indexedmzML
schema: <indexList> name attribute will be enumerated to “spectrum” or
“chromatogram” to disallow other creative values

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

- New schema is posted on the web. The tiny file has been updated.

- Eric will update the web site announcing the change and update hyperlink

- Eric will update the other files

- Post by Andreas Schoenegger on Jun 9

- Richard will address this by updating the schema

- How do we handle lock mass corrections?

- We should assemble list of calibrants and make them specific terms

- Bruker uses Lithium Formiate; others?

- Jim will find out what Thermo is using

- Jim will talk to someone later today and compile a list of calibrants
commonly used

- Matt will contact David Anderson and Mike Ashton and ask about a date in
lieu of checksum

- Need to test FAIMS support in mzML

- According to folks at ISB, addition of “compensation voltage” is all
that’s needed

- Eric will try create a real example

- Have the questions from Steffen on Apr 7 and Apr 8 all been resolved?

- Sometime in the future spend some time on a dozen CV terms per call to
resolve them.

- Other items?



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2) MIAPE-MS revision

- Document is ready to be submitted, but..

- We need to have 3 examples to go along with a document submission

- Until we provide the examples, it is not officially in the document
process

- We can use the sample MIAPE-compliant mzML file

- Pierre-Alain will contact Juan-Pablo to see if he has some suitable
examples in Proteo-Red

- Pierre-Alain has received an example from Proteo-Red

- Richard will look into PRIDE to see if there may be a good example there

- Pierre-Alain is looking through PRIDE to find a good example.

- The last example would be a MIAPE compliant mzML document

- Looking in Peptidome might be an alternative for finding a nicely
annotated dataset

- Waiting to sync with MIAPE-MSI as well

- Keep working on our documents and when we’re ready, see if we should wait

- We also need to coordinate the creation of MIAPE-Quant

- When officially in the process, send out submitted document to journal
editors and everyone else to get the word out



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3) TraML development

- Version 0.9.4 released and is available at
http://www.psidev.info/index.php?q=node/405

- Specification document is updated. Please examine. Is it ready for
submission?


http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt will sent out a sample file

  - Matt hopes to finish the C# bindings sometime

  - Eric will try validating with his tools

  - ISB implementation in ATAQS nearly done

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

  - Jim will work to update this soon

  - Eric will also contact Amol to discuss TraML implementations

  - David Cox at Sciex will test implement?

  - Eric will follow up with David

- Are we ready to update validator page?:
http://www.psidev.info/index.php?q=node/304

- Eric emailed submission materials to PSI editors



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4) PSI session at World HUPO in Sydney

- PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric

- Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS

- Abstract is accepted

- Other reports?



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5) Working with ASMS on controlled vocabulary

- no update



Next meeting:

- In 2 weeks? July 13?