Re: [Psidev-ms-dev] TraML 0.9.3 draft released

[Steffen N. <sne...@ip...>]

On Tue, 2010-01-05 at 00:12 -0800, Eric Deutsch wrote:

> Please examine the materials and respond.

- The header line still refers to 0.9.2
- The documents mentions analysisXML in 2.2, 
  with an invalid URL.

- <Target> (include and exclude, for that matter) 
  doesn't have the notion of an m/z window:
  1) You might be not interested in everything below 200Da
  2) Depending on the instrument it might be necessary 
  to use broader isolation windows for sufficient 
  product ion intensities.
  
- <Target> (include and exclude, for that matter) 
  doesn't have the notion of <RetentionTime> to 
  (optionally) restrict a RT (window)

- 3.30 says "Precursor (Q1) of the transition" should add "target"

- <configuration> could allow an isolation width, 
  as an alternative to the mz min/max I mentioned above.
  mzML had some lengthy min/max vs. width discussions last year ...

- The name "Tra(nsition)ML" suggests that the format is 
  for (TripleQuad) MRM experiments. For "1.3 Use Cases" I'd like to add
  more explicitly the description of a tandemMS (and MS^n) run.

  To me, TraML can also describe a "method" for an MS run.
  For Bruker QTof, such a description lives in files such as 
  method.m/microTOFQAcquisition.method, but they're (so far)
  quite undocumented.

Yours,
Steffen

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
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