[Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

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

[updated agenda]

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

 

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Agenda:

 

- Wilfred suggests:

  (A) Have "MS1 spectrum" and "MSn spectrum" [This is the current situation]


  (B) Have "MS1 spectrum" (or appropriate synonym), "MS2 spectrum" (or
appropriate synonym), and "MSn spectrum" [restrict n >= 3] 

  (C) Have "MSn spectrum" only and rely on mslevel to specify 1, 2, etc. 

  My vote is for option (B) given the high occurrence of MS1 spectra and MS2
spectra, with option (C) coming in second. 

 

- Desire to revisit id="" index="" nativeID="" (see Dec 8 Re:
[Psidev-ms-dev] spectrum identifiers on list)

  I am reluctant to reopen this can of snakes

- I propose that we keep all three attributes as previously decided

  index is xsd:nonNegativeInteger

  id is xs:ID

  nativeID is xs:string with an xsd uniqueness constraint on it

  One may not have two different representations of the same scan in a
single file (document this!)

 

- Approve/modify Eric's proposal of usage of index, id, nativeID within and
from outside mzML

 

- Approve/modify "mass resolution" and "mass resolving power" terms proposed
by Wilfred

 

- Approve/modify Eric's proposal on "other" and "unknown" terms

 

- Post of the recommended change to the spectrum wrt spectrum and
acquisition 12/5 1:17a

 

- componentList to become optional and InstrumentConfiguration required?

 

- How do we/can we deal with optional elements that are required by MIAPE?-
Validator (TOPP validator and EBI validator)

 

- Is this what we want and is it a problem for validators as Marc suggests?

  "isolation m/z lower limit" is PART_OF the description of an "isolation
window"

     "isolation window is PART_OF the description of a "precursor"

        "precursor is PART_OF the description of a "spectrum"

  Can the mapping file not specify that <isolationWindow> must have two
cvParams

  which are PART_OF "isolation window"?

  What to do?

 

- Other issues lost in the shuffle or in the tracker?

  http://sourceforge.net/tracker/?atid=1126041
<http://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

 

- Who will implement the schema changes we discussed?

- Who will update the CV?

- Who will update the mapping file?

- Who will update the documentation?

 

- TraML

 

- Next call? 23rd?