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

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

Hi everyone, this is a reminder for the PSI MSS WG teleconference call
tomorrow, Tuesday, at the usual time.



The primary agenda item will be to finish discussion of the TraML reviews
and set action items to address them.



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 accepted to MCP:


http://www.mcponline.org/content/early/2010/08/17/mcp.R110.000133.full.pdf+html

- 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

- How do we handle lock mass corrections?

- Eric should test FAIMS support in mzML

- Eric should test a recent file with multiple fragmentation types to see if
they are properly labeled

- 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

- TraML version 0.9.4 is available at
http://www.psidev.info/index.php?q=node/405

- TraML was submitted to PSI document process

- Reviews are back, see attached. Discuss how to address these concerns

- Implementations? Please update to 0.9.4 and test

  - Matt has implemented in ProteoWizard complete to 0.9.4

  - Matt has finished the C# bindings which will enable Skyline support

  - Matt will sent out a sample file

  - 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

  - Eric will also contact Amol to discuss TraML implementations

  - Dave Cox at Sciex will test implement?

  - Need to add two new terms

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



----

4) PSI session at World HUPO in Sydney

- Eric presented on the work of the group: mzML 1.1, TraML 0.9.4, MIAPE-MS



----

5) Improving the controlled vocabulary

- There is a todo list based on a previous discussion

- Need someone with some time to work on it



6) SRM analysis guidelines and format

- At a “Data Quality Metrics” workshop in Sydney before World HUPO (hosted
by NCI), there was strong support to try to develop a set of guidelines for
reporting of SRM experiments as there currently are none. A working group
was identified at the meeting. Eric will organize some discussions on this.

- It was also proposed that PSI work on a standard format for the reporting
of SRM experiment analysis. There was some support for this. This is
distinct from mzML, which holds the chromatograms. It is distinct from TraML
which holds the input transitions. It might have some overlap with
mzQuantML. This should be discussed and a subgroup identified.





Next meeting:

- In 1 week? Oct 19?