Re: [Psidev-ms-dev] PSI-MSSWG call in 8 hr

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

Hi everyone, here are my notes from the telecon. Thank you for your
participation. Please let me know if I forgot/misunderstood anything:

 

Meeting minutes 2008-03-04 9:00am PST

 

Present: Darren, Jim, Matt, Lennart, Josh, Eric

 

- Eric's most recent nativeID proposal is accepted except for the format
of the value, which should be:

  nativeID="19"

  nativeID="2,6,5"

  nativeID="run1,3,4"

  nativeID=""run1,2",3,4"

 

- possible charge state suggestion is fine with folks:

  - 0-1 "charge state"

  XOR

  - 2-N "possible charge state"

 

- Come up with an example of how we want summed spectra to look:

- one file that includes original scan and a summed spectrum

 

- in old mzXML, we can have different start_scan and end_scan. How do we
encode that?

 

- defaultArrayLength proposal is fine

 

- Jim has some examples of files with PDA data

  He will come up some examples of this

  Perhaps encoded as the MS spectrum as usual <spectrum index="27"
nativeID="19"> and then another

  <spectrum index="28" nativeID="PDA19"> with a spectrum type "PDA
spectrum"

 

- Jim will also come up MALDI data examples for us

 

- agreed that we rename selectionWindow to scanWindow as this is a
misnomer

- add optionally to <ionSelection>, all 2 new cvParams "selection window
m/z lower limit"

  and "selection window m/z upper limit" for the *true* fragmentation
selection window start and stop

 

- agreed change acqNumber to acquisitionNumber

 

- What to do with msLevel?

  agreed make it a cvParam next to spectrum type instead of a attribute
of <spectrum>

  because for example a PDA spectrum will have no msLevel

 

- state that index should be for seeking rather than cataloguing.

  So no msLevel in the index

  Index should be *complete* so it could be used for a list of items to
seek to

  but should contain only identifiers, not attributes/metadata

  - Start a thread on this to discuss more

 

- Matt will send <chromatogram> example since he is working on these now

 

- Next meeting indeed March 25 as on schedule.  This is *3* weeks from
now, because of US HUPO

- Maybe a few of us could meet and chat at US HUPO although unlikely
anything official.

 

 

 

 

 

________________________________

From: Eric Deutsch 
Sent: Tuesday, March 04, 2008 1:08 AM
To: 'Mass spectrometry standard development'
Cc: Eric Deutsch
Subject: PSI-MSSWG call in 8 hr

 

Hi everyone, here is a reminder of the call coming up in 8 hr. Dial-in
information is:

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

 

The agenda will be to discuss all the items that have come up recently.
I list them as:

 

- Latest nativeScanReference proposal

- using defaultArrayLength attribute in <spectrum> but allow override in
binaryDataArray

- Allow new "possible charge state" term in <ionSelection> multiple
times

- Frederick suggestion that selectionWindow should really be scanWindow.
selectionWindow is something different, and by the way, where is it, we
really need that, too.

- MS^E example

- msLevel

- chromatograms

 

The schedule is still:

 

Schedule:

-----------------------

Jan 25: mzML reviews returned. Official community review complete.

Feb  5: mzML telecon 9:00am PST

Feb 19: mzML telecon 9:00am PST

Mar  4: mzML telecon 9:00am PST

Mar 17: US HUPO meeting 

Mar 25: mzML telecon 9:00am PST

Apr  8: mzML telecon 9:00am PST

Apr 23: PSI meeting in Toledo

May

Jun 1-5: ASMS - Must be done and advertising it here!