[Psidev-ms-dev] Teloc minutes 20090623

[Lennart M. <len...@eb...>]

Dear PSI-MS Enthusiasts,


Please find the meeting minutes of the 20090623 PSI-MS phoneconference 
below.


Telephone conference 20090623

  Participants:
    - Jim Shofstahl
    - Pierre-Alain Binz
    - Marc Sturm
    - Darren Kessner
    - Eric Deutsch
    - Matt Chambers
    - Lennart Martens (notes)

  Agenda:
    - Numerical precision; topic highlighted by Steve Stein: binary 
floats did not come with (implicit) precision
       + Eric suggested an optional additional array containing 
precision, but this might be overkill
       + Matt suggests that precision is typically a derived variable 
(e.g. from instrument resolution)
       + Steve's precision is likely to come from meta-analysis (in the 
spectrum library)
       + Pierre-Alain points out that the libraries want to move from 
nominal values to more precise values, where this precision can vary 
depending on the datapoint
       + Matt asks whether this means that experimental peaks that are 
(confidently) assigned are corrected or replaced by theoretical vlaues
       + Eric mentions that mzML was not intended for spectral libraries 
in design, and that we had this discussion before. Maybe we should 
therefore also consider the output from vendors, and see if they need to 
store such information.
       + Jim says that Thermo can provide m/z resolution information in 
addition to the actual m/z values. But this information is currently not 
used nor readily available in the Thermo export tool.
       + Darren asks whether a binary representation for a fixed 
floating point number (like 15.00) exists? Nobody knows.
       --> Propose to add an m/z precision array and ask wheter we need 
an intensity precision array type in mzML on the list (similar to the 
signal-to-noise array type we already have)
    - Validation of example files
       + Steffen's file does not yet validate, due to a missing term in 
the CV (absorbance units)
       --> Eric wil contact the Unit Ontology maintainer to add this 
term to the Unit Ontology
    - CV terms changes
       + PSI-PI people have been adding some terms, and Marc has 
committed some changes to MALDI laser units (together with Andreas)
    - Converters
       + Several implementations are coming along nicely, and various 
people are working with vendors on implementations
    - MIAPE MS compared to MCP Guidelines
       + A revised version will be discussed with the various journals, 
this version should be finalized this week by Pierre-Alain, and Sandra 
will create a SurveyMonkey survey as well.
    - TraML development
       + Eric hasn't gotten around to sopending much time on this 
lately, but will get around to updating the schema in the next days.
    - Upcoming phone conference schedule
       --> Will be decided each Monday, based on the number of topics we 
have lined up
    - Manuscript about mzML
       + Nature Biotechnology back-to-back with mzIdentML seems like a 
real option right now, based on commmunication with Nat Biotech editors
       --> Lennart takes care of writing the draft.

Cheers,

lnnrt.