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[Psidev-ms-dev] PSI-MSS WG call deferred 1 week
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From: Eric D. <ede...@sy...> - 2010-06-07 17:34:12
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Hi everyone, due a schedule change, I am unable to make it to tomorrow’s PSI-MSS WG call. Let’s meet a week later instead, Jun 15 8am PDT, unless this causes some serious problem? Thanks, Eric *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Tuesday, May 18, 2010 9:38 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call notes Present: Matt, Richard, Jim, Eric Agenda: 1) mzML 1.1.0 - Manuscript has been reviewed and the comments addressed and resubmitted. - The editors have come back and asked for the inclusion of a “tangible example of an application" and then it will be acceptable for publication. Response in progress. + Richard suggests a jzmzml as an application + Matt suggests quantification, wiff files, spectrum annotation - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink + Eric will update the other files - How do we handle lock mass corrections? - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using - Jim will look at an old email and send out the information + Jim will ask around at ASMS and compile a list of calibrants commonly used - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML + Eric will talk to Chris at ISB - Other items? + Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? + Sometime in the future spend some time on a dozen terms per call to resolve them. ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We 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 - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - 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 + ProteoWizard implementation is complete to 0.9.4 + Matt has sent out a sample file + Matt hopes to finish the C# bindings this week + Eric will try validating with his tools - Andreas will implement in OpenMS and update on-line validator + Sadly Andreas has perished in a car accident and is no longer with us - 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 follow up with David - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is in preparation and will be sent out shortly ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - JuanAn maybe can’t go? - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? - Perhaps some of us try to meet at ASMS briefly? - Note that there will be a Computational Mass Spectrometry/Bioinformatics for MS meeting at ASMS - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention Center - Featuring Alexey Nesvizhskii and David L. Tabb ---- 5) Working with ASMS on controlled vocabulary - no update + Matt suggested slowly working through purgatory at these calls. Eric will prep. Next meeting: - In 3 weeks? June 8? Regular time + agreed *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, May 17, 2010 9:59 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call reminder <1 hr time shift!> Hi everyone, I now have a conflicting meeting at the usual 8am timeslot, and next week is ASMS, so I’d like to try to squeeze in the call one hour later. I hope most participants can be tolerant of this. So, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136 09:00 San Francisco 12:00 New York 17:00 London 18:00 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 the comments addressed and resubmitted. - The editors have come back and asked for the inclusion of a “tangible example of an application" and then it will be acceptable for publication. Response in progress. - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink - How do we handle lock mass corrections? - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using - Jim will look at an old email and send out the information - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - Other items? ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We 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 - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - 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 in preparation and will be sent out shortly ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - JuanAn maybe can’t go? - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? - Perhaps some of us try to meet at ASMS briefly? - Note that there will be a Computational Mass Spectrometry/Bioinformatics for MS meeting at ASMS - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention Center - Featuring Alexey Nesvizhskii and David L. Tabb ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 3 weeks? June 8? |
