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Re: [Psidev-ms-dev] PSI-MSS WG call reminder
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From: Eric D. <ede...@sy...> - 2010-04-06 15:43:42
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Present: Richard, Matt, Steffen, Eric 1) mzML 1.1.0 - Manuscript has been reviewed and generally positive. Reviewers concerns can be addressed. In progress. + Lennart did a first pass at responding to the reviewers + Eric is trying to finish - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” + Richard will get password from JuanAn and make the update - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 + Waiting for schema to be posted - How do we handle lock mass corrections? Someone will make an example - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using + No progress on lock mass corrections - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum + They are looking into hashing objects. No resolution yet. - Need to test FAIMS support in mzML + Eric will work with those generating some data at ISB - Add term for “compensation voltage” to support FAIMS data + Matt will add the proposed term - Other items? ---- 2) MIAPE-MS revision - Need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - When officially in the process, send out submitted document to journal editors and everyone else to get the word out + Ask Pierre-Alain about the mzML MIAPE-MS mapping file ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard + Matt will try to finish this in the next 3 weeks - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? + Eric will ping Jim and David - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is also in preparation - Additional example files + Steffen will generate an XCMS example and post ---- 4) PSI workshop in Seoul - Andy Jones presented the report. - Other reports? - Perhaps try to meet at ASMS briefly ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes + No progress for the moment. They will meet at ASMS in June Next meeting: - In 3 weeks? Apr 27? + Yes, Tue Apr 27 8am PDT (in 3 weeks) + Possible CPTAC conflict *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, April 05, 2010 9:46 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call reminder Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=4&year=2010&hour=16&min=0&sec=0&p1=136 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been reviewed and generally positive. Reviewers concerns can be addressed. In progress. - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? - Jim will find out what Thermo is using - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - Add term for “compensation voltage” to support FAIMS data - Other items? ---- 2) MIAPE-MS revision - Need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is also in preparation ---- 4) PSI workshop in Seoul - Andy Jones presented the report. - Other reports? - Perhaps try to meet at ASMS briefly ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes Next meeting: - In 3 weeks? Apr 27? |
