Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call notes

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

Notes from today's call.

Present: Fredrik, Jim, Wilfred, Pierre-Alain, Steffen, Eric, Darren, Marc

 

+ Steffen will check that his examples still work

+ ICMS: International Conference on Mass Spectrometry soon in Bremen in
September. Steffen may do a poster

+ German Mass Spectrometry conference occurred early March: there was a
presentation on imaging mzML (imzML)

+ imzML is still based on mzML 1.0 but they will update it to mzML 1.1

 

- Approve scanWindow dx:ScanWindowType -> dx:paramType

+ Eric fixed that. No objections here

- Approve isolation window target m/z, lower offset, upper offset

+ Fine

+ Eric will obsolete the older terms

- unit.obo rev 1.19 issue to be solved

+ Fixed in 1.20. Eric will update psi-ms.obo to reflect 1.20

- scan time -> scan start time change, and elution time added

+ Marc did this. Fine.

- CV items

+ Wilfred says "dwell time" is an awkward location in the CV. Should be
moved to spectrum type?? Fredrik agrees.

+ Wilfred will email out his recommended nativeID format to the list and it
will be included as a term

+ The definition for run should be discussed and possibly modified for
MALDI. Discuss with Matt and Lennart.

- Mapping file items

+ Eric will make sure that the mapping file changes from Wilfred of 3/15 are
applied to SVN

- Example files updated?

+ Eric will make the changes to the CV and mapping file and email when done.

+ Marc and Fredrik will update validators and email

+ Darren and Wilfred and Steffen and Fredrik will update and validate
examples and email with done

+ Then Eric will update the documentation and email when done

- No more open issues?

+ No, except SRM file size, see below.

- Submit!

- Turku plans

+ Fredrik, Marc, Jim, Pierre-Alain, Eric will be there

+ Add to agenda also a discussion of SRM

+ We discussed the history of the current design of SRM encoding

+ Wilfred and Jim will try to come up with an arsenal of examples of
original files and mzML converted files, showing the inflation of file size
and we can consider ways to improve this at Turku

- Next call? March 31?

+ Yes, same time.

 

 

  _____  

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Tuesday, March 10, 2009 8:22 AM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: PSI-MSS WG Tuesday call notes

 

Present: Matt, Jim, Marc, Eric, Darren

 

Topics:

 

- Address latest issues

- Wilfred's issue of <product> needs <selectIonList>

+ Eric will contact Wilfred and Fredrik and Matt. Must come up with an
example use case

+ Eric will update the mapping file per Wilfred's suggestion

 

- Example files updated?

+ Matt and Darren will update the examples today

+ Marc added volt per meter to the electric field strength to CV

 

- Submit!

- A few straggling unit issues from Marc

+ Orbitrap units should just be number of counts

+ Darren will go ahead and create one example file requested by Marc with 6
spectra all encoded in the six different possible datatypes and post it.

 

- Next call? March 17?

+Yes, if needed 8am PDT.

 

 

 

 

 

 

  _____  

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Tuesday, March 03, 2009 8:55 AM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: PSI-MSS WG Tuesday call notes

 

Present: Matt, Fredrik, Eric, Jim, Darren, 

 

Topic:

- Decision of where to put nativeID format <cvParam>

+ Adopt Darren's suggestion of 2/26 3:44p: always only specify nativeID
format in <sourceFile> and use

  "no id format" term is N/A

+ Eric make sure documentation says what to do with a folder of files: each
file included as source files

+ Darren will adjust the example files

+ Eric will add the CV term & email Darren

+ Eric will adjust mapping file

- Decision on sourceFileRefList

+ Remove <sourceFileRefList> element and below

+ Add <run> attribute defaultSourceFileRef=

+ Document that in the case of multiple files in a folder, or wiff &
wiff.scan, specify the key file (wiff, func001.dat, analysis.yep)

+ Can specify all files as <sourceFiles> at the top, but only reference the
key one.

+ Matt will make the xsd changes and check in and email Eric

+ Darren will update examples & email Eric

+ Eric will update the Documentation with latest schema and also rules about
which file to reference

- Example files updated?

+ Darren will update and post

+ Fredrik will update and post

- Ready to submit?

+ When these things are done, then Eric will submit

- A few straggling unit issues from Marc

+ Darren will ask Jim directory about orbi/FT intensitities

+ Defer rest until next week

- Next call? March 10?

+ Yes. Probably 8am PST March 10

 

 

 

 

 

 

  _____  

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Monday, March 02, 2009 5:15 PM
To: 'Mass spectrometry standard development'
Cc: 'Eric Deutsch'
Subject: PSI-MSS WG Tuesday call reminder

 

Hi everyone, the next PSI Mass Spectrometry Standards Working Group call
will be Tuesday 8am PST:

 

(this is back to our regular time. I don't *think* there's a conflict with
PSI SG)

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=3
<http://www.timeanddate.com/worldclock/fixedtime.html?day=3&month=3&year=200
9&hour=16&min=0&sec=0&p1=136> &month=3&year=2009&hour=16&min=0&sec=0&p1=136

 

08:00 San Francisco

11:00 New York

16:00 London

17:00 Western Europe

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

Generic international: +44 2083222500 (UK number)

 

access code: 297427

 

Agenda:

- Decision of where to put nativeID format <cvParam>

- Decision on sourceFileRefList

- Example files updated?

- Ready to submit?

- A few straggling unit issues from Marc

- Next call? March 10?