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

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

Notes from teleconference on Apr 5, 2011



Present: Florian, Eric, Matt, Pierre-Alain, Jim,





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

- Steffen feels there probably only minor changes required for GC-MS.
Probably only mostly just some terms like “travel time” and the like.

- Currently the ANDI format is most often used for GC-MS, but it seems out
of date and is the format that would be replaced.

- Steffen attended a metabolomics conf at EBI and will report

- 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

+ Need a term for LTQ Orbitrap Velos. Matt will add.

+ Jim will send along additional missing instruments

+ Eric has problems with SF CVS

+ Need definition for Steffen’s proposed “second column modulation time”

- Other items?



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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 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 generated from ProteoWizard

  - Eric will try validating with his tools

  - ISB implementation in ATAQS is 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?

  - Brendan’s comments were found and sent to the list

  - Need to add two new terms

- Change <Validation> to <ValidationStatus>

- Fix <Configuration> to (1..N)

- What about MS3 support?

- Steffen points out that just adding another <Product> tag isn’t enough.
What if there are different collision energies for MS2 and MS3?

- Seems like there was agreement to move <Interpretation>, <Prediction>,
<ConfigurationList> into <Product>, thereby allowing (requiring!) separate
entries for each <Product> entry. For 99% of cases, this is just a trivial
move of elements.

- Discussion ensued about <Product> should have “isolation window target
m/z” or “selection window target m/z”.  Are we isolating (pure filter) or
selecting (scanning in a range)? Ran out of time. Continue on email or next
time.

+ Agreed that <Precursor> is “isolation window” and <Product> is a
“selection window”?

+ To support MS3, Add an <intermediateProduct> element

+ Eric will put together an example of that and email it out

+ Discussed Brendan’s Review

+ Matt will email out how mzIdentML can support non Unimod modifications

- 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

- Progress will continue at the workshop

+ Trying to get MIAPE-compliant mzML file

+ One example from PRIDE

+ One example article from Proteomics

+ Ask Juan Pablo for MIAPE example



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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.

- Richard will ask David Ovelleiro to send a note to the list on his efforts

- There is a list of action items from a previous call

- Email from David Ovelleiro this morning

+ David will present at the meeting next week



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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 person next week in Heidelberg