[Psidev-ms-dev] No call tomorrow

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

Hi everyone, I regret the late notice, but I just returned from a trip and
am unable to do the call tomorrow as we had planned. Let us defer it until
next week.

There has been some progress on the mzML manuscript, however. We have a
almost-final draft and we are hoping to submit by the end of the week.

Regards,
Eric


> -----Original Message-----
> From: Matthew Chambers [mailto:mat...@va...]
> Sent: Thursday, January 21, 2010 8:08 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] PSI-MSS WG call reminder
> 
> 
> Conference call notes:
> 
> Present: Matt, Jim, Ree?, Mark, Steffen, Eric
> 
> 1) mzML 1.1.0
> 
> - Manuscript now in active preparation
> + draft available in a couple weeks
> 
> - Matt will release updated 1.1.1 of indexedmzML schema: <indexList>
> name attribute will be enumerated to "spectrum" or "chromatogram"
> + not yet done
> 
> - Matt will update the example files to reference mzML 1.1.0 but
> indexedmzML 1.1.1
> + not yet done
> 
> - Andreas will add "Replaced-by" field to the obsoleted MaRiMba term
> + done
> 
> - Matt added new terms for ABI TOF/TOF T2D file format
> + done
> 
> - How do we handle lock mass corrections? Matt will make an example
> + Steffen wants lock mass spectra to be marked so they can be segregated
> + Need an example of what lock mass spectra would look like in mzML,
> also what do corrected spectra look like (e.g. processingMethod)?
> + Steffen will start a ML thread with ideas on the topic.
> + CompassXport beta version supports mzML
> 
> - Other items?
> 
> 
> ----
> 
> 2) MIAPE-MS revision
> 
> - Pierre-Alain has sent out the revised MIAPE-MS draft 2.94 document to
> the list
> - Everyone: Please examine MIAPE-MS 2.94 in Pierre-Alain Binz's email on
> 2009-12-22 and respond with comments
> - Deadline is Jan 12, after which the document will be submitted to the
> PSI document process
> + Pierre-Alain will address minor comments and send doc process
> 
> ----
> 
> 3) TraML development
> 
> - Current version 0.9.3 is available at
> http://www.psidev.info/index.php?q=node/405
> - Matt suggest changing "frag: y ion" to "product: y ion"
> - But Andreas points out that the "frag" is supposed to differentiate
> search parameter from resulting
> - Andreas will rephrase all the definitions for "frag: y ion" to be better
> + done
> 
> - Fredrik sent out an inclusion list example. Everyone look and comment.
> - Andreas also sent out an example
> + not yet reviewed
> 
> - What do we do about specifying retention times, i.e. where to allow
> <RetentionTimeList> (see 1/14)
> + because of semantic differences between predicted/observed retention
> times (e.g. provided by public transition lists), should we move local
> retention time to transition or configuration?
> + local retention time under transition can override local retention
> time in Peptide/Compound
> + Eric will summarize the discussion to the list. Add <RetentionTime> to
> <Transition> and <Target>
> 
> - Do we try to merge <Transition> and <Target>?
> + Keep them separate for now.
> + Discussed the scope of TraML. We agreed that we would keep TraML 1.0
> limited to transitions and an additional add-on for inclusion/exclusion
> lists. Steffen proposes a future TraML 2.0 or MethodsML that tries to
> tackle a unified instrument input configuration or "methods file" format.
> 
> - Implementations?
>   - Matt will implement in ProteoWizard
>   + mostly done
>   - Andreas will implement in OpenMS and update on-line validator
>   + done
>   - ISB implementation in ATAQS nearly done
>   - Jim will implement as a test
>   - David Cox at Sciex will test implement?
> - Are we ready to update validator page?: http://www.psidev.info
> 
> Next meeting:
> + Eric is unavailable in two weeks, next meeting is in 3 weeks on
> February 9th at regular time.
> 
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