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

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

Notes from today’s teleconference.



Present: Matt, Jim, Richard, Eric, Pierre-Alain, Alexey,



Agenda:

1) Meetings and workshops

- PSI Spring Workshop San Diego March 12-14 (+ProteomeXchange 15-16)

- Note nearby US HUPO March 4-7 and ABRF March 17-20

-



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2) mzML 1.1.0

- mzML for metabolics

+ We need some CV terms for GC-GC coupling:

  + “modulation time” ?

  + There was a discussion a few months ago. Try to revive this.

- mz5 and mzDB

+ mz5 is exact schema for mzML but with HDF5

+ Matt is using it and performance is good

+ Developed by Steen Lab and contributed to ProteoWizard

+ mzDB uses SQLite as back end and uses mzML snippets for metadata

- digital signatures

-



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3) TraML development

- TraML version 0.9.5 is available at
http://www.psidev.info/index.php?q=node/405

- TraML was resubmitted to PSI document process

- Currently in community review period

+ Clarify with Christian when this is officially over

- Discuss response to 5th reviewer

+ Clarify the scope of TraML at the beginning of the response as the list of
transitions between vendor software, repositories,

+ Amplify the response to “no one wants to parse .sky files”

+ Clarify that “neutral loss scans” and “precursor ion scans” are not
supported in section 1.3.5



- Discuss Alexey’s use case and needed terms

+ Signal to noise probably better than intensity even

+ Alexey’s proposal seems quite reasonable to try

+ Eric will send an email with the terms proposed



+ Steffen has an R package for writing inclusion lists

+ Steffen will find a hyperlink to it and we will post on the TraML dev page



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4) MIAPE-MS revision

- Special call on Thursday for MIAPE - *



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5) Improving the controlled vocabulary

- Proposed “command line parameters” CV term and implications

+ This sounds quite sensible to us. Follow up with an email to list

+ Would this include the executable/path or just everything after that.
Probably after.

+ Matt points out that pretty much all options are encoded in the file. But
gathering them is difficult to recreate the step

+ Everyone agreed that it was useful to add

- CV term requests from Sean



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6) SRM analysis guidelines and format

- Review MIAPE-Quant for SRM

- Review mzQuantML for SRM

+ We need to create a sample mzQuantML document for an SRM experiment. Who
will try?

+ Steffen may try



Next meeting:

- Tue Oct 11 8am PDT?

+ Yes