[Psidev-ms-dev] PSI-MSS WG call minutes

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

Hi everyone, here are the minutes for the PSI-MSS WG telecon of
2008-06-10.

 

Present: Matt, Darren, Eric, Lennart, Pierre-Alain, Jim

 

- ASMS

+ Douglas Slotta has implemented mzML in their C++ toolkit

+ Jim talked to Steve Musser at FDA. They are considering accepting mzML
as a format to avoid cherry-picked spectra, but it would need some kind
of non-text audit trail information. Randy will talk with Vish about
this talk. Follow up.

+ There was a suggestion at ASMS that we move toward ISO certification
for the standard to promote adoption

+ Users are very positive about a single format

 

- schema

+ No major schema changes planned

+ Let's keep a list of minor possibly desirable changes to make if there
needs to be an important change

+ One desirable addition is retention time in the index

 

- MIAPE example document?

+ Done and posted except for switching criteria and parameters for
creating peaklists

+ Pierre-Alain and Jim will get together and finish this

 

- CV status

+ Darren has sent a proposal for of datatype and relationship
"has_units". It's good. Proceed with all terms.

+ "scan time" is one example

+ OBO-Edit will write out all terms including imported terms unless told
not to. That can be done with filters.

+ Darren will post a recipe on how to filter out non-MS terms

+ Darren is still figuring out how to get OBO-Edit to write out "import"
statements

+ Darren will email John Richter-Day about that

+ Current CV version is 1.0.0

+ As Darren or anyone makes changes, increment the version number.

+ Darren will try to import the unit ontology from its source

+ Would a side effect of this prevent OBO-Edit from opening a file w/o
Internet? Darren will check

+ Normally all terms going forward now should be deprecated (deleted in
OBO-Edit terms)

+ However, the unit terms could be destroyed. Eric will destroy them.

                               

- CV template updates to vendors

+ Start another round of vendor updates

+ Some software organized by vendor

 

- documentation

+ Documentation is up to date

+ Images in documentation still mention 0.99.12. Should update to 1.0.0

+ Lennart will regenerate embedded figures and send to Eric who will
update

 

- website

+ Post the mapping file directly

+ Should we set up an mzML.org?

+ Instead of maintaining a separate page, set up a redirect?

 

- mzML support information table

+ Definitely post it on the web site

+ Bruker will likely support mzML. Find out their plans

 

- validator

+ Validator will be a little delayed. There are many back-end changes
due to the MI group

+ Does the validator check that if there is an acquisition list, then
there would be a combination type (like sum of spectra) provided?

+ We will allow spectrum representation (like centroid/profile) in the
fileContent section

+ Need to incorporate the information in the OBO file (datatypes and
units)

+ Need to fix up the mapping file rules

+ Lennart hopes to have coding update done at the end of this week and
then we need help from everyone to update the mapping file

+ Maybe need a rule that if a spectrum and if a mass spectrum, the need
mz array and similar

+ Need some sort of unit for intensity arrays

+ At the moment, we do not require any units for the array type. We
should add that.

+ Darren will explore that while adding has_units to CV

 

- example files

+ Matt will take a stab at MALDI example and post it

+ Eric will remove tiny4 and point to "small" which includes LTQ-FT demo
usage

+ Fredrik sent to Eric nice examples of dta -> mzML and plgs -> mzML.
Eric will post.

+ Matt will generate an example MGF -> mzML using pwiz and post

+ Jim will send Eric & Matt some example RAW files and converted files
(including PDA, SRM)

 

- Amsterdam

+ Pierre-Alain will do the presentation of the mzML talk during main
conference

+ PSI session during the congress at Sunday 17th 9:30a-12

+ Tentative presenter at PSI session is Jim Shofstahl with backups of
Randy and Pierre-Alain

 

- Next call

+ Switch call time to *Monday* morning 9am PDT due to conflicts

+ Same time in two weeks on June 23rd