[Psidev-ms-dev] additional CV terms

[Kessner, D. E. <Dar...@cs...>]

Hi all,

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I came across a piece of info that we use in our lab that is not
currently represented in the CV: scan event.

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Thermo uses the "scan event" (integer) to represent a set of scan
settings.  The user chooses what settings are associated with a
particular scan event.  The instrument cycles through the scan events
repeatedly during a run.  The scan event is saved with the other scan
meta-data in the Thermo RAW file.

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For example, our QC runs on an LTQ-FT look something like this:

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scan#   scan event   settings

  1             1              Ion trap survey scan

  2             2              FT survey scan

  3             3              ms2  523.77@35

  4             4              ms2  810.41@35

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  5             1              Ion trap survey scan

  6             2              FT survey scan

  7             3              ms2  523.77@35

  8             4              ms2  810.41@35

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  9             1              Ion trap survey scan

 10            2              FT survey scan

 11            3              ms2  523.77@35

 12            4              ms2  810.41@35

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=2E..

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We include the scan event as a <scan> attribute in our mzXML files.  We
can then filter out and inspect scans by scan event with various command
line tools and scripts that we use for quality control.

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We'll want to have a CV term for the MSData library as well.

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Darren

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Darren Kessner

Scientific Programmer

Dar...@cs...

310-423-9538

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Spielberg Family Center for Applied Proteomics

Cedars-Sinai Medical Center

http://www.sfcap.cshs.org/

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