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

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

Hi everyone, this is a reminder for the PSI MSS WG teleconference call
tomorrow, Tuesday. Please note the times below. Since USA and Europe are out
of sync on daylight savings time, the times are a little different than
usual.



08:00 San Francisco

11:00 New York

15:00 London         ß   !!

16:00 Geneva        ß    !!



+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)



access code: 297427 #



Agenda:

1) PSI Spring Workshop April 11-13

- Collaborative efforts with the PI WG on mzIdentML, mzQuantML, CV

- Finishing TraML

- Drafting SRM experiment guidelines

- Drafting a format for SRM experimental results

- MIAPE-MS finalization

- MIAPE-Quant work?

- Adjacent to the ProteomeXchange workshop

- Please attend and encourage attendance



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2) mzML 1.1.0

- We have been contacted by Vladimir Likic, who has said that he is
representing some portions of the metabolomics community and they are
interested in seeing if mzML would be a good fit for them as a
next-generation format. See:
http://bioinformatics.bio21.unimelb.edu.au/mzml.html

- Other outstanding todo items:

  - 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?



----

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 and partially addressed.Still outstanding todo items

- 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



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4) 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

- 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



----

5) Improving the controlled vocabulary

- There is a todo list based on a previous discussion

- Need someone with some time to work on it

- Some folks from PRIDE have expressed the desired to clean up the CV. Work
with them.



----

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 2 weeks Mar 29?