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From: Eric D. <ede...@sy...> - 2008-11-11 08:02:26
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PST (in 8 hr): http://www.timeanddate.com/worldclock/fixedtime.html?day=11 <http://www.timeanddate.com/worldclock/fixedtime.html?day=11&month=11&year=2 008&hour=16&min=0&sec=0&p1=136> &month=11&year=2008&hour=16&min=0&sec=0&p1=136 + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 Topics: - Schema changes: no one protested, so we should go ahead and make the changes? - change location of <spectrum> cvParams - scan/acquisition issue. Multiple scans inside acquisition? We need examples of what we want - Update rev to mzML 1.0.1 and update all documentation and examples - nativeID format: Resolved. Add to documentation - Marc has raised a number of issues to discuss. He has volunteered to maintain an open issues list - dataProcessingRef - <scanWindow> questions from Marc? - Removing/fixing scanning method child terms in CV - Export of CV to OLS - Validator (TOPP validator and EBI validator) - Next call |
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From: Eric D. <ede...@sy...> - 2008-11-24 21:00:06
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PST: http://www.timeanddate.com/worldclock/fixedtime.html?day=25 <http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=11&year=2 008&hour=16&min=0&sec=0&p1=136> &month=11&year=2008&hour=16&min=0&sec=0&p1=136 + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 Unrefined list of things to discuss: - Who will write the revised xsd for the changes we have agreed to make? - We need to update all example files. Who will? - Need to update all the documentation Who will? Eric will - Schema changes: no one protested, so we should go ahead and make the changes - change location of <spectrum> cvParams - scan/acquisition issue. Multiple scans inside acquisition? We need examples of what we want - Update rev to mzML 1.0.1 and update all documentation and examples - nativeID format: Resolved? Add to documentation - Marc added data types for several CV terms - Created "selected m/z" term instead of making "m/z" and "mass-to-charge" ratio different terms - Mapping file has been updated - Fredrik created a subpage for the sematic validator: http://www.psidev.info/index.php?q=node/390 - Marc has created the issue tracker for us: http://sourceforge.net/tracker/?atid=1126041 <http://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse> &group_id=65472&func=browse - Must implement a required nativeID definition in the fileDescription - Create a term for "center m/z" for? <cvParam cvRef="MS" accession="MS:1000XXX" name="center m/z" value="800"/> <cvParam cvRef="MS" accession="MS:1000023" name="isolation width" value="200"/> Pierre-Alain points out 2008-11-18 4:39a PST that we had favored start/end m/z instead of center/width - David Sparkman joined in a lively discussion of resolving power and resolution. Was there a clear outcome? - Is nativeID put to rest? Still a few ambiguities to discuss RE Matt's post 2008-11-17 - Marc suggests a schema change to softwareParam - Marc brings up sample state CV term 2008-11-14 - Need better documentation for raw scan/microscan/summed spectra 2008-11-13 - Matt has suggested (2008-11-24) new terms for charge state calc and precursor recalc - dataProcessingRef - <scanWindow> questions from Marc? - Removing/fixing scanning method child terms in CV - Export of CV to OLS - Validator (TOPP validator and EBI validator) - Next call |
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From: Eric D. <ede...@sy...> - 2009-06-30 01:25:29
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=30 <http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=6&year=20 09&hour=16&min=0&sec=0&p1=136> &month=6&year=2009&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 - Outstanding items - Manuscript ---- 2) mzML implementations catalog ---- 3) MIAPE-MS revision - Have revised document to discuss at ASMS ---- 4) TraML development - Updates pending - Implementations? |
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From: Marc S. <stu...@gm...> - 2009-06-30 14:35:02
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Hi all, I won't make it to the phone conference today. I read the manuscript and think it is already quite good. The image has to be adapted to the current schema though. Best, Marc Eric Deutsch wrote: > > Hi everyone, the next PSI Mass Spectrometry Standards Working Group > call will be Tuesday 8am PDT: > > > > http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=6&year=2009&hour=16&min=0&sec=0&p1=136 > <http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=6&year=2009&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 > > - Outstanding items > > - Manuscript > > > > ---- > > 2) mzML implementations catalog > > > > ---- > > 3) MIAPE-MS revision > > - Have revised document to discuss at ASMS > > > > ---- > > 4) TraML development > > - Updates pending > > - Implementations? > > > > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > |
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From: Fredrik L. <Fre...@im...> - 2009-07-06 14:42:24
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Hi All, Just a quick note to tell that the hand crafted SRM example has been updated to use chromatograms instead of spectra, according to the 1.1.0 specification. Please tell me if you spot any errors. Also, the binary arrays in this example does not make sense, so it would be nice to have a real SRM example file available online (pwiz conversion?) The file (also linked from the spec site): http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans/MRM_example_1.1.0.mzML?format=raw Regards Fredrik |
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From: Matthew C. <mat...@va...> - 2009-07-06 15:14:10
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The Agilent test data included with ProteoWizard in both native and mzML format (it's used as a unit test) should serve nicely as example mzML data. Currently all the data is QQQ. There is SRM and SIM currently supported, and there's a NL example too but Reader_Agilent doesn't support that yet (thus the file is just a single TIC). Some of the SRM data is mixed with MS2 data, although I don't think they are MIDAS experiments. Reader_Agilent also supports precursor ion spectra, but that example was too big so I nixed it. Agilent has approved us using and distributing their example data. I wish other vendors had similar redistributable test data sets. I should be getting a couple of good Thermo example files from Mike MacCoss soon as well - an LTQ example with MS1-3 and zoom scans, and a TSQ example with SRM, SIM, PI, and NL. Not a very sensible test, but very good for a unit test. ;) Here's the download for Agilent: http://proteowizard.svn.sourceforge.net/viewvc/proteowizard/trunk/pwiz/pwiz/data/vendor_readers/Agilent/Reader_Agilent_Test.data.tar.bz2 If anybody on the list has small Agilent QTOF data (less than a megabyte after compression) I'd like to include that for testing and example purposes as well. Thanks, Matt Fredrik Levander wrote: > Hi All, > > Just a quick note to tell that the hand crafted SRM example has been > updated to use chromatograms instead of spectra, according to the 1.1.0 > specification. > Please tell me if you spot any errors. Also, the binary arrays in this > example does not make sense, so it would be nice to have a real SRM > example file available online (pwiz conversion?) > The file (also linked from the spec site): > http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans/MRM_example_1.1.0.mzML?format=raw > > Regards > > Fredrik > > |
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From: Eric D. <ede...@sy...> - 2009-07-14 06:52:09
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=14 <http://www.timeanddate.com/worldclock/fixedtime.html?day=14&month=7&year=20 09&hour=16&min=0&sec=0&p1=136> &month=7&year=2009&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 - Outstanding items - Policy for source directories: finalize and document - Absorbance unit - proposal to add terms "m/z precision array" and "intensity precision array": def number of significant digits - - Manuscript - AniML ---- 2) MIAPE-MS revision - Have revised document to discuss at ASMS ---- 3) TraML development - Updates pending - Try splitting "transition predicted from consensus spectrum ion trap" into two terms - Do we want to add the mzML sourceFileList section? - <evidence> is not pretty - - Implementations? |
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From: Eric D. <ede...@sy...> - 2009-07-14 16:54:26
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Hi everyone, here are the notes from today's call Present: Matt, Marc, Jim, Darren, Eric 1) mzML 1.1.0 - Outstanding items - Policy for source directories: finalize and document + The policy will be that all of the files needed to encode of the spectra will be listed. Individual implementations should know what files to include. If this cannot easily be determined, it would not be harmful to include all files in the subdir, perhaps after filtering out obvious contaminating files such as mzData and MGF files that may have been introduced. - Absorbance unit + This has been added to the unit ontology - proposal to add terms "m/z precision array" and "intensity precision array": def number of significant digits + Eric will write the proposal and send it out for comment - version attribute discussion + There appear to be two proposals: 1) require the version number attribute and control the values they can take on; 2) let the version attribute atrophy and make it policy to get the version from the schemaLocation attribute. The attendees were evenly split on which approach to take. Eric will email the proposals in a new thread and we would vote. - Manuscript + The manuscript has been submitted to NBT and how we wait. - AniML + Eric attended the last AnIML phone conference and described mzML and our controlled vocabulary. AnIML is moving forward and includes many data types beyond mass spec. As they develop mass spec support, they will be looking closely at mzML. ---- 2) MIAPE-MS revision - What is the state of MIAPE-MS and the preparation for the journals meeting at world HUPO? ---- 3) TraML development - Updates pending - Try splitting "transition predicted from consensus spectrum ion trap" into two terms - Do we want to add the mzML sourceFileList section? - <evidence> is not pretty - Implementations? + Eric will send out the next revision soon _____ From: Eric Deutsch [mailto:ede...@sy...] Sent: Monday, July 13, 2009 11:52 PM 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=14 <http://www.timeanddate.com/worldclock/fixedtime.html?day=14&month=7&year=20 09&hour=16&min=0&sec=0&p1=136> &month=7&year=2009&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 - Outstanding items - Policy for source directories: finalize and document - Absorbance unit - proposal to add terms "m/z precision array" and "intensity precision array": def number of significant digits - - Manuscript - AniML ---- 2) MIAPE-MS revision - Have revised document to discuss at ASMS ---- 3) TraML development - Updates pending - Try splitting "transition predicted from consensus spectrum ion trap" into two terms - Do we want to add the mzML sourceFileList section? - <evidence> is not pretty - - Implementations? |
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From: Eric D. <ede...@sy...> - 2009-07-28 06:03:16
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=28 <http://www.timeanddate.com/worldclock/fixedtime.html?day=28&month=7&year=20 09&hour=16&min=0&sec=0&p1=136> &month=7&year=2009&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 - Outstanding items - Policy for source directories: finalize and document - Use of version attribute - proposal to add terms "m/z precision array" and "intensity precision array": def number of significant digits - Manuscript ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO ---- 3) TraML development - Updates pending - Try splitting "transition predicted from consensus spectrum ion trap" into two terms - Do we want to add the mzML sourceFileList section? - <evidence> is not pretty - Implementations? |
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From: Shofstahl, J. <jim...@th...> - 2009-07-28 14:33:47
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Eric, I won't be able to attend this morning due to Jury Duty. Jim Shofstahl From: Eric Deutsch [mailto:ede...@sy...] Sent: Monday, July 27, 2009 11:03 PM To: 'Mass spectrometry standard development' Cc: 'Eric Deutsch' Subject: [Psidev-ms-dev] 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=28&month=7&year=2009&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 - Outstanding items - Policy for source directories: finalize and document - Use of version attribute - proposal to add terms "m/z precision array" and "intensity precision array": def number of significant digits - Manuscript ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO ---- 3) TraML development - Updates pending - Try splitting "transition predicted from consensus spectrum ion trap" into two terms - Do we want to add the mzML sourceFileList section? - <evidence> is not pretty - Implementations? |
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From: <ede...@sy...> - 2009-08-10 22:22:08
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=11&month=8&year=2009&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 - Outstanding items - Still no decision on the version attribute business - Policy for source directories: finalize and document - proposal to add terms “m/z precision array” and “intensity precision array”: def number of significant digits - Manuscript - BioPortal is now automatically pulling our CV from CVS. See: http://bioportal.bioontology.org/ontologies?filter=PSI ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO ---- 3) TraML development - New version 0.9.0 posted at dev page: http://www.psidev.info/index.php?q=node/405 - Significant updates - Most everything is a cvParam - “transition predicted from consensus spectrum ion trap” split into two terms - Added sourceFileList from mzML? - HTML doc, spec doc, toy example, mapping file, CV all updated - Implementations? - What do we do with the <interpretation> cvParams? |
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From: <ede...@sy...> - 2009-08-13 20:49:29
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Present: Lennart, Darren, Jim, Eric, Steffen, Matt, Pierre-Alain 1) mzML 1.1.0 - Outstanding items - Still no decision on the version attribute business + Proposal is to say in the spec doc that the schemaLocation says mzML1.1.0.xsd - Policy for source directories: finalize and document + Eric will write this in the spec - proposal to add terms “m/z precision array” and “intensity precision array”: def number of significant digits + Eric will do this + Should there a more global way of specifying the resolution? - Manuscript + No news yet - BioPortal is now automatically pulling our CV from CVS. See: http://bioportal.bioontology.org/ontologies?filter=PSI - Our CV is now on OLS as well - Terms from Kalhardt Change: fourier transform ion cyclotron resonance mass spectrometer To: fourier transform ion cyclotron resonance analyzer + Add below that: quadrupole FTICR? Ask for clairifcation + Pierre-Alain will follow up and determine what changes there should be. + Lennart will label old Mass Spec CV as Obsolete + As a result of investigating the CV, it turns out the analyzer section can do with a thorough read-through. Matt will give it a look + Matt will update the ion trap portion of the CV + What about FTICR? Should that be under cyclotron? ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO + Sandra has sent out a survey to PSI folks for feedback before sending out to editors + If you haven’t received this email and want to, email Pierre-Alain + touches are being done on the MIAPE document ---- 3) TraML development - New version 0.9.0 posted at dev page: http://www.psidev.info/index.php?q=node/405 - Significant updates - Most everything is a cvParam - “transition predicted from consensus spectrum ion trap” split into two terms - Added sourceFileList from mzML? - HTML doc, spec doc, toy example, mapping file, CV all updated - Implementations? - What do we do with the <interpretation> cvParams? Next call in two weeks *From:* ede...@sy... [mailto:ede...@sy...] *Sent:* Monday, August 10, 2009 3:22 PM *To:* Mass spectrometry standard development *Cc:* ede...@sy... *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=11&month=8&year=2009&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 - Outstanding items - Still no decision on the version attribute business - Policy for source directories: finalize and document - proposal to add terms “m/z precision array” and “intensity precision array”: def number of significant digits - Manuscript - BioPortal is now automatically pulling our CV from CVS. See: http://bioportal.bioontology.org/ontologies?filter=PSI ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO ---- 3) TraML development - New version 0.9.0 posted at dev page: http://www.psidev.info/index.php?q=node/405 - Significant updates - Most everything is a cvParam - “transition predicted from consensus spectrum ion trap” split into two terms - Added sourceFileList from mzML? - HTML doc, spec doc, toy example, mapping file, CV all updated - Implementations? - What do we do with the <interpretation> cvParams? |
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From: Eric D. <ede...@sy...> - 2009-08-25 06:51:45
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=25 <http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=8&year=20 09&hour=16&min=0&sec=0&p1=136> &month=8&year=2009&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 - Outstanding items ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO ---- 3) TraML development - New version 0.9.0 posted at dev page: http://www.psidev.info/index.php?q=node/405 - Implementations? - What do we do with the <interpretation> cvParams insufficiency problem? |
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From: Shofstahl, J. <jim...@th...> - 2009-08-25 14:44:07
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Eric, I may be a little late for today's call. I have another call from 7:30AM to 8:30AM. Jim Shofstahl From: Eric Deutsch [mailto:ede...@sy...] Sent: Monday, August 24, 2009 11:51 PM To: 'Mass spectrometry standard development' Cc: 'Eric Deutsch' Subject: [Psidev-ms-dev] 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=25&month=8&year=2009&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 - Outstanding items ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO ---- 3) TraML development - New version 0.9.0 posted at dev page: http://www.psidev.info/index.php?q=node/405 - Implementations? - What do we do with the <interpretation> cvParams insufficiency problem? |
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From: Fredrik L. <Fre...@im...> - 2009-09-08 15:07:44
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No call today? Eric Deutsch wrote: > > Hi everyone, the next PSI Mass Spectrometry Standards Working Group > call will be Tuesday 8am PDT: > > > > http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=8&year=2009&hour=16&min=0&sec=0&p1=136 > <http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=8&year=2009&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 > > - Outstanding items > > > > ---- > > 2) MIAPE-MS revision > > - Have revised document to discuss at HUPO > > > > ---- > > 3) TraML development > > - New version 0.9.0 posted at dev page: > > http://www.psidev.info/index.php?q=node/405 > > > > - Implementations? > > - What do we do with the <interpretation> cvParams insufficiency problem? > > > > > > > |
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From: <ede...@sy...> - 2009-09-10 20:38:02
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Hi everyone, sorry I forgot to send around a notice. It was my last day of vacation and I wasn't able to get it together. Some recent developments: - We have been given the opportunity to submit the mzML manuscript to MCP. So we will work on preparing the manuscript and submitting it. Look for a draft soon. - World HUPO is fast approaching so we should review the plans for posters and talks. - imzML now has a web site: http://www.imzml.org/ If there are any other announcements or concerns, please email them. I would be especially interested in feedback on TraML. It appears that next week I have an unexpected trip and will be on a plane at the usual time, so unless we have important topics and someone else will lead the call, I suggest we have our next call the Tuesday before HUPO. Regards, Eric > -----Original Message----- > From: Fredrik Levander [mailto:Fre...@im...] > Sent: Tuesday, September 08, 2009 8:08 AM > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] PSI-MSS WG call reminder > > No call today? > > Eric Deutsch wrote: > > > > Hi everyone, the next PSI Mass Spectrometry Standards Working Group > > call will be Tuesday 8am PDT: > > > > > > > > > http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=8&yea > r=2009&hour=16&min=0&sec=0&p1=136 > > > <http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=8&ye > ar=2009&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 > > > > - Outstanding items > > > > > > > > ---- > > > > 2) MIAPE-MS revision > > > > - Have revised document to discuss at HUPO > > > > > > > > ---- > > > > 3) TraML development > > > > - New version 0.9.0 posted at dev page: > > > > http://www.psidev.info/index.php?q=node/405 > > > > > > > > - Implementations? > > > > - What do we do with the <interpretation> cvParams insufficiency > problem? > > > > > > > > > > > > > > > > > ----------------------------------------------------------------------- > ------- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: <ede...@sy...> - 2009-09-22 06:10:36
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=22&month=9&year=2009&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 - HUPO poster - HUPO Saturday PSI session presentation - HUPI Monday talk - Outstanding items ---- 2) MIAPE-MS revision - Have revised document to discuss at HUPO ---- 3) TraML development - New version 0.9.0 posted at dev page: http://www.psidev.info/index.php?q=node/405 - HUPO poster - HUPO Saturday PSI session presentation - Implementations? - What do we do with the <interpretation> cvParams insufficiency problem? |
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From: <ede...@sy...> - 2009-09-22 15:52:36
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Present: Andreas, Fredrik, Matt, Eric
Discussion of TraML/TarML to better support ordinary inclusion/exclusion
lists
Eric will propose to add to schema:
<targetIncludeList>
<target id=”” peptideRef=””>
<precursor>…</precursor>
<configurationList>…</configurationList>
</target>
…
</targetIncludeList>
<targetExcludeList>
<target id=”” peptideRef=””>
<precursor>…</precursor>
<configurationList>…</configurationList>
</target>
…
</targetExcludeList>
1) mzML 1.1.0
- Manuscript : in preparation for submission to MCP
- HUPO poster: PAB currently reviewing it
- HUPO Saturday PSI session presentation by PAB
- HUPO Monday talk by Eric
- Outstanding items
- some discussion about non-integer charge values from Proteios
- Andreas wrote a proposal on 9/1. Add two mapping file rules. No
conclusion on last item. Keep in mind for future revisions
- Matt agrees to fix the CV hierarchy problem near spectrum type as
described 9/1 by Andreas
----
2) MIAPE-MS revision
- Have revised document to discuss at HUPO
----
3) TraML development
- New version 0.9.0 posted at dev page:
http://www.psidev.info/index.php?q=node/405
- HUPO poster by Eric
- HUPO Saturday PSI session presentation by Eric
- Implementations? Let’s make a push in October to get some implementations
going and prepare official submission.
- What do we do with the <interpretation> cvParams insufficiency problem?
No meeting next week due to HUPO Congress.
Meet again in two weeks, same time.
Eric
*From:* ede...@sy... [mailto:ede...@sy...]
*Sent:* Monday, September 21, 2009 11:10 PM
*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=22&month=9&year=2009&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
- HUPO poster
- HUPO Saturday PSI session presentation
- HUPI Monday talk
- Outstanding items
----
2) MIAPE-MS revision
- Have revised document to discuss at HUPO
----
3) TraML development
- New version 0.9.0 posted at dev page:
http://www.psidev.info/index.php?q=node/405
- HUPO poster
- HUPO Saturday PSI session presentation
- Implementations?
- What do we do with the <interpretation> cvParams insufficiency problem?
|
|
From: Eric D. <ede...@sy...> - 2009-10-20 06:59:18
|
Hi everyone, sorry for the late notice, but I cannot be at the PSI Mass Spectrometry Standards Working Group call tomorrow. Let's cancel and discuss progress next week instead. Thanks, Eric |
|
From: Eric D. <ede...@sy...> - 2009-10-06 06:30:07
|
Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=06 <http://www.timeanddate.com/worldclock/fixedtime.html?day=06&month=10&year=2 009&hour=16&min=0&sec=0&p1=136> &month=10&year=2009&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) World HUPO Congress results - Saturday PSI session with mzML and TraML presentations - mzML 1.1 poster and presentation - TraML 0.9 poster - MIAPE-MS discussions with journals - Other? ---- 2) mzML 1.1.0 - Manuscript plans? Aim for end of October? - Other? ---- 2) MIAPE-MS revision - Discussion with journal editors was Monday. Results are in. ---- 3) TraML development <http://www.psidev.info/index.php?q=node/405> http://www.psidev.info/index.php?q=node/405 - Aim to submit specification to document process by end of October - Implementations? - What do we do with the <interpretation> cvParams insufficiency problem? - Add a new <targetList> section for inclusion and exclusion precursor targets - TarML? There already is a TARML in the universe.. Temporal Authorization Rule Markup Language - Maybe Andreas can help with inclusion/exclusion examples - David Cox at Sciex would like to do some test implementation |
|
From: <ede...@sy...> - 2009-10-06 15:43:26
|
+ Present: Matt, Jim, Fredrik, Andreas, Eric Agenda: 1) World HUPO Congress results - Saturday PSI session with mzML and TraML presentations - mzML 1.1 poster and presentation - TraML 0.9 poster - MIAPE-MS discussions with journals - Other? + Eric gives a summary of the results from HUPO ---- 2) mzML 1.1.0 - Manuscript plans? Aim for end of October? - Other? + MS3+ spectra topic from list on 2009-09-22: + As long as the MS(n-1) scan is available, then the previous precursor is available in the previous scan + Eric: update documentation on how MS3+ precursor information is to be encoded + How do we encode the case where one has an ambiguous charge state and one wants to encode both hypotheses in the mzML + Matt will come up with an example of how that might look in mzML ---- 2) MIAPE-MS revision - Discussion with journal editors was Monday. Results are in. + Discuss with Pierre-Alain + MIAPE-MS update ---- 3) TraML development http://www.psidev.info/index.php?q=node/405 - Aim to submit specification to document process by end of October - Implementations? - What do we do with the <interpretation> cvParams insufficiency problem? - Add a new <targetList> section for inclusion and exclusion precursor targets - TarML? There already is a TARML in the universe.. Temporal Authorization Rule Markup Language - Maybe Andreas can help with inclusion/exclusion examples + Andreas is working on updating OpenMS to 0.9 + Put <targetIncludeList> and exclude in a container <targetList> with CV term to indicate precendence. + Eric will send out email on that. - David Cox at Sciex would like to do some test implementation + Andreas will update implementation + Jim will update his implementation + Matt will update his implementation in ProteoWizard + Meet again in two weeks *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, October 05, 2009 11:30 PM *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=06&month=10&year=2009&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) World HUPO Congress results - Saturday PSI session with mzML and TraML presentations - mzML 1.1 poster and presentation - TraML 0.9 poster - MIAPE-MS discussions with journals - Other? ---- 2) mzML 1.1.0 - Manuscript plans? Aim for end of October? - Other? ---- 2) MIAPE-MS revision - Discussion with journal editors was Monday. Results are in. ---- 3) TraML development http://www.psidev.info/index.php?q=node/405 - Aim to submit specification to document process by end of October - Implementations? - What do we do with the <interpretation> cvParams insufficiency problem? - Add a new <targetList> section for inclusion and exclusion precursor targets - TarML? There already is a TARML in the universe.. Temporal Authorization Rule Markup Language - Maybe Andreas can help with inclusion/exclusion examples - David Cox at Sciex would like to do some test implementation |
|
From: <ede...@sy...> - 2009-10-26 19:18:31
|
Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=27&month=10&year=2009&hour=16&min=0&sec=0&p1=136 (Note: Europe is off daylight savings time, but the US is still on it, so I have opted to retain the usual time in Europe, but shifted the meeting 1 hour later in the US. I normally have a conflict at this time, but do not tomorrow. I hope this is okay with most participants) 09:00 San Francisco 12:00 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 - Outstanding items ---- 2) MIAPE-MS revision - Revised document. Discuss changes. ---- 3) TraML development - Version 0.9.0 still posted at dev page: http://www.psidev.info/index.php?q=node/405 - Proposal to add a new <targetList> module to TraML for ordinary inclusion lists - Addition of <retentionTimeList> construct - Enhanced AA mass modification encoding - Returning peptide sequence back to an attribute - Add <proteinRef> as an element to allow multiple - Split retention time window into “retention time start” and “retention time end” cvParams - Fredrik proposes to put local retention times under transition instead of peptide/compound - Andreas suggests a term for describing the source of an RT (prediction, database, experimental…) - What do we do with the <interpretation> cvParams insufficiency problem? |
|
From: Eric D. <ede...@sy...> - 2009-11-17 07:45:07
|
Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=17 <http://www.timeanddate.com/worldclock/fixedtime.html?day=17&month=11&year=2 009&hour=16&min=0&sec=0&p1=136> &month=11&year=2009&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 in preparation - Were Shimadzu items handled? - Other items? ---- 2) MIAPE-MS revision - Discussion with journal editors was Monday. Results are in. - We need to work toward a new release of MIAPE-MS ---- 3) TraML development - Version 0.9.1 is available at <http://www.psidev.info/index.php?q=node/405> http://www.psidev.info/index.php?q=node/405 - Should we switch to first-letter capital for all elements as seems to be the custom everywhere else in PSI except mzML? - Aim to submit specification to document process by end of November - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - What do we do with the <interpretation> cvParams insufficiency problem? - Maybe Andreas can help with inclusion/exclusion examples - There are some mapping file validation errors that need to be fixed (mapping file problems) - Are we ready to update validator page?: <http://www.psidev.info/index.php?q=node/304> http://www.psidev.info/index.php?q=node/304 |
|
From: Eric D. <ede...@sy...> - 2009-11-17 16:39:56
|
Present: Matt, Eric, Pierre-Alain 1) mzML 1.1.0 - Manuscript in preparation - Were Shimadzu items handled? + Matt will add Shimadzu Biotech software & MALDI solutions - Other items? + What about lock mass data? + Add a “lock-mass corrected spectrum” term that can be added to each scan if appropriate? Matt will send proposal + Summary of msconvert support for conversion to mzML. Latest summary: http://proteowizard.sourceforge.net/technical/formats/ + 5 major vendors fully supported. Missing: ABI TOF-TOF, Shimadzu, Hitachi ---- 2) MIAPE-MS revision - Discussion with journal editors happened in Toronto. - We need to work toward a new release of MIAPE-MS + Pierre-Alain will make revisions and present document to WG for discussion by Dec 1 ---- 3) TraML development - Version 0.9.1 is available at http://www.psidev.info/index.php?q=node/405 - Should we switch to first-letter capital for all elements as seems to be the custom everywhere else in PSI except mzML? - Aim to submit specification to document process by end of November - Implementations? - Matt will implement in ProteoWizard by end of November? - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - What do we do with the <interpretation> cvParams insufficiency problem? - Maybe Andreas can help with inclusion/exclusion examples - There are some mapping file validation errors that need to be fixed (mapping file problems) + Eric will fix these issues - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, November 16, 2009 11:45 PM *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=17&month=11&year=2009&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 in preparation - Were Shimadzu items handled? - Other items? ---- 2) MIAPE-MS revision - Discussion with journal editors was Monday. Results are in. - We need to work toward a new release of MIAPE-MS ---- 3) TraML development - Version 0.9.1 is available at http://www.psidev.info/index.php?q=node/405 - Should we switch to first-letter capital for all elements as seems to be the custom everywhere else in PSI except mzML? - Aim to submit specification to document process by end of November - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - What do we do with the <interpretation> cvParams insufficiency problem? - Maybe Andreas can help with inclusion/exclusion examples - There are some mapping file validation errors that need to be fixed (mapping file problems) - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 |
|
From: Eric D. <ede...@sy...> - 2009-11-30 21:59:33
|
Hi everyone, due to a schedule change, I cannot host this week’s conference call. Let’s defer until next week. Pierre-Alain, can we discuss the MIAPE-MS revision next week? We are making progress here on our TraML implementation. Any other bits on progress on that front to report? Thanks, Eric *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Tuesday, November 17, 2009 8:40 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call notes Present: Matt, Eric, Pierre-Alain 1) mzML 1.1.0 - Manuscript in preparation - Were Shimadzu items handled? + Matt will add Shimadzu Biotech software & MALDI solutions - Other items? + What about lock mass data? + Add a “lock-mass corrected spectrum” term that can be added to each scan if appropriate? Matt will send proposal + Summary of msconvert support for conversion to mzML. Latest summary: http://proteowizard.sourceforge.net/technical/formats/ + 5 major vendors fully supported. Missing: ABI TOF-TOF, Shimadzu, Hitachi ---- 2) MIAPE-MS revision - Discussion with journal editors happened in Toronto. - We need to work toward a new release of MIAPE-MS + Pierre-Alain will make revisions and present document to WG for discussion by Dec 1 ---- 3) TraML development - Version 0.9.1 is available at http://www.psidev.info/index.php?q=node/405 - Should we switch to first-letter capital for all elements as seems to be the custom everywhere else in PSI except mzML? - Aim to submit specification to document process by end of November - Implementations? - Matt will implement in ProteoWizard by end of November? - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - What do we do with the <interpretation> cvParams insufficiency problem? - Maybe Andreas can help with inclusion/exclusion examples - There are some mapping file validation errors that need to be fixed (mapping file problems) + Eric will fix these issues - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, November 16, 2009 11:45 PM *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=17&month=11&year=2009&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 in preparation - Were Shimadzu items handled? - Other items? ---- 2) MIAPE-MS revision - Discussion with journal editors was Monday. Results are in. - We need to work toward a new release of MIAPE-MS ---- 3) TraML development - Version 0.9.1 is available at http://www.psidev.info/index.php?q=node/405 - Should we switch to first-letter capital for all elements as seems to be the custom everywhere else in PSI except mzML? - Aim to submit specification to document process by end of November - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - What do we do with the <interpretation> cvParams insufficiency problem? - Maybe Andreas can help with inclusion/exclusion examples - There are some mapping file validation errors that need to be fixed (mapping file problems) - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 |
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