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From: Eric D. <ede...@sy...> - 2010-04-27 15:42:27
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Hi everyone, here are the notes from the telecon: Present: Richard, Jim, Eric, Matt, Pierre-Alain, 1) mzML 1.1.0 - Manuscript has been revised and the revision sent out for comment. To be resubmitted in 2 days. - 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 + 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 + Matt will get to it first think next week - 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 + Jim is almost done. Will get create metabolomics file with the software - 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 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 - Other reports? - Perhaps try to meet at ASMS briefly ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 3 weeks? May 18? + Yes. May 18 8am PDT *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, April 26, 2010 4:43 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=27&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 revised and the revision sent out for comment. To be resubmitted in 2 days. - 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 Formiate; 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 - 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 - Waiting to sync with MIAPE-MSI as well - 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 session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Other reports? - Perhaps try to meet at ASMS briefly ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 3 weeks? May 18? |
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From: Eric D. <ede...@sy...> - 2010-06-15 14:31:38
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Hi everyone, sorry I forgot yesterday to send around the reminder for the call. Let's go ahead with the call 30 minutes from now as scheduled. 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 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> 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_specificationDocu ment.doc> http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocum ent.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> 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? |
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From: Eric D. <ede...@sy...> - 2010-06-15 15:32:29
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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 + Eric will write this and send back in - 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 - Post by Andreas Schoenegger on Jun 9 + Richard will address this by updating the schema - 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 talk to someone later today 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 and Kristian at ISB + According to folks at ISB, addition of “compensation voltage” is all that’s needed + Eric will try create a real example - 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 CV 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 will sent out a sample file + Matt hopes to finish the C# bindings sometime + Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 + Jim will work to update this soon + Eric will also contact Amol to discuss TraML implementations - 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, Sandra?, Henning. - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? ---- 5) Working with ASMS on controlled vocabulary - no update + Matt suggested slowly working through purgatory at these calls. Eric will prep. Next meeting: - In 2 weeks? June 29? Regular time + agreed *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Tuesday, June 15, 2010 7:31 AM *To:* 'Mass spectrometry standard development' *Cc:* 'Eric Deutsch' *Subject:* PSI-MSS WG call reminder Hi everyone, sorry I forgot yesterday to send around the reminder for the call. Let’s go ahead with the call 30 minutes from now as scheduled. 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 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? |
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From: Steffen N. <sne...@ip...> - 2010-06-16 08:36:41
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On Tue, 2010-06-15 at 08:32 -0700, Eric Deutsch wrote: > 3) TraML development ... > - Implementations? Please update to 0.9.4 and test There is now a preview of TraML export for xcms, for an example (validated by OpenMS for 0.9.4) http://msbi.ipb-halle.de/~sneumann/xcmsTraML.xml Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: Eric D. <ede...@sy...> - 2010-06-17 06:18:42
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Hi Steffen, this looks great, many thanks! The only problem is that there is no CV term for XCMS. Would you suggest one? (with definition!) so you don't need to use the custom software term? Thanks! Eric > -----Original Message----- > From: Steffen Neumann [mailto:sne...@ip...] > Sent: Wednesday, June 16, 2010 1:37 AM > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] PSI-MSS WG call notes > > On Tue, 2010-06-15 at 08:32 -0700, Eric Deutsch wrote: > > 3) TraML development > ... > > - Implementations? Please update to 0.9.4 and test > > There is now a preview of TraML export for xcms, > for an example (validated by OpenMS for 0.9.4) > > http://msbi.ipb-halle.de/~sneumann/xcmsTraML.xml > > Yours, > Steffen > > -- > IPB Halle AG Massenspektrometrie & Bioinformatik > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 http://msbi.bic-gh.de > 06120 Halle Tel. +49 (0) 345 5582 - 1470 > +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > -------------------------------------------------------------------------- > ---- > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Steffen N. <sne...@ip...> - 2010-06-17 07:34:22
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On Wed, 2010-06-16 at 23:18 -0700, Eric Deutsch wrote: > The only problem is that there is no CV term for XCMS. Then it is about high time: [Term] id: MS:100XXXX name: XCMS software def: "XCMS (A Bioconductor package to analyse high-throughput mass spectrometry data." [PSI:MS] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: Steffen N. <sne...@ip...> - 2010-06-29 21:13:03
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On Wed, 2010-06-16 at 23:18 -0700, Eric Deutsch wrote: > The only problem is that there is no CV term for XCMS. Would you suggest > one? (with definition!) so you don't need to use the custom software term? Done. The file http://msbi.ipb-halle.de/~sneumann/xcmsTraML.xml now has a proper Software cvParam. The OpenMS validator is currently not working (Permission denied in /nfs/.../TraML/index.php) but it *should* validate. Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: Eric D. <ede...@sy...> - 2010-06-28 23:33:51
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: 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 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 - Eric will write this and send back in - 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 - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today 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 - According to folks at ISB, addition of “compensation voltage” is all that’s needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - 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 - 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 has implemented in ProteoWizard complete to 0.9.4 - Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - 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 - Eric emailed submission materials to PSI editors ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 2 weeks? July 13? |
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From: Eric D. <ede...@sy...> - 2010-06-29 15:29:15
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Present: Richard, Jim, Eric, Pierre-Alain 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 - Eric will write this and send back in - 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 - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today 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 - According to folks at ISB, addition of “compensation voltage” is all that’s needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - Other items? ---- 2) MIAPE-MS revision - We have the needed 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 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 - 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 + Pierre-Alain will contact Proteo-Red again about comments + Hope that MIAPE-MS can be submitted to document process in July + Might we start a draft of MIAPE-Quant in parallel with the start of development of mzQuantML? + MIAPE-Quant will probably have different sections for each major type of quanitification ---- 3) TraML development - 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 has implemented in ProteoWizard complete to 0.9.4 - Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - 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 - Eric emailed submission materials to PSI editors + A few minor things to fix and then resubmit ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 2 weeks? July 13? + Yes *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, June 28, 2010 4:34 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: 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 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 - Eric will write this and send back in - 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 - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today 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 - According to folks at ISB, addition of “compensation voltage” is all that’s needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - 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 - 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 has implemented in ProteoWizard complete to 0.9.4 - Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - 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 - Eric emailed submission materials to PSI editors ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 2 weeks? July 13? |
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From: Eric D. <ede...@sy...> - 2010-07-13 08:17:19
|
Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: 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) Review of controlled vocabulary file terms Have your OBO-Edit open to the latest psi-ms.obo Next meeting: - In 2 weeks? July 27? |
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From: Eric D. <ede...@sy...> - 2010-07-13 17:29:16
|
Present: Fredrik, Matt, Richard, Jim, Eric
Next meeting:
July 27 same time: confirmed
Today’s discussion centered around recent and needed changes to the CV
- PSI web site maintenance:
- Update OBO-Edit hyperlinks
- Add browse link to OLS, too
- OBO-Edit 2.1 complains: non-critical warning: nth generation product ion
spectrum (MS:1000339) generated 1 warning:
The term nth generation product ion spectrum links to the obsolete term
product ion spectrum
- term “run attribute” has no parent and is floating at the top. Fix. Move
under “object attribute” for now.
- Change the term “standard” and its children to be a more generic
“reference” although add term “approved standard”
- reference
RT norm reference
H-PINS RT norm reference
- Add Krohkin peptides reference
- Regarding peptide and protein, okay to keep current structure but add in
Chebi relationship
- chemical compound = polyatomic entity
- peptide = polypeptide
- protein = protein
- But strangely, Chebi defines “polypeptide” as being at least 10 AA long.
There is no plain “peptide”. So what is a 9 AA peptide in Chebi? Seems like
just a “molecule” which is odd. Why 10?? Our current definition of “peptide”
is at least 2 AAs. How do we resolve this? Contact Marcus Ennis (mennis@ebi)
*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Tuesday, July 13, 2010 1:17 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:
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) Review of controlled vocabulary file terms
Have your OBO-Edit open to the latest psi-ms.obo
Next meeting:
- In 2 weeks? July 27?
|
|
From: Eric D. <ede...@sy...> - 2010-08-10 08:40:47
|
Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: 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 resubmitted. - 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 - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today 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 - According to folks at ISB, addition of “compensation voltage” is all that’s needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - Other items? ---- 2) MIAPE-MS revision - We have the needed 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 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 - 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 + Pierre-Alain will contact Proteo-Red again about comments + Hope that MIAPE-MS can be submitted to document process in July + Might we start a draft of MIAPE-Quant in parallel with the start of development of mzQuantML? + MIAPE-Quant will probably have different sections for each major type of quanitification ---- 3) TraML development - TraML is currently undergoing formal review in the document process - Version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 - Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - 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 ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? ---- 5) Work on improving CV - Review action items from last teleconference 2010-07-13 Next meeting: - In 3 weeks? Aug 31? |
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From: Eric D. <ede...@sy...> - 2010-08-10 17:20:25
|
Present: Richard, Jim, Matt, Eric 1) mzML 1.1.0 - Manuscript has been resubmitted. - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - Eric will update the web site announcing the change and update hyperlink - Eric will update the other files - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today and compile a list of calibrants commonly used + Answer is perhaps that what the Thermo calibration compound is is not well known - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - According to folks at ISB, addition of “compensation voltage” is all that’s needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - Other items? + Eric should test a recent file with multiple fragmentation types to see if they are properly labelled ---- 2) MIAPE-MS revision - We have the needed 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 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 - 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 - Pierre-Alain will contact Proteo-Red again about comments - Hope that MIAPE-MS can be submitted to document process in July - Might we start a draft of MIAPE-Quant in parallel with the start of development of mzQuantML? - MIAPE-Quant will probably have different sections for each major type of quanitification ---- 3) TraML development - TraML is currently undergoing formal review in the document process - Version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 + Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime + Matt has finished the C# bindings - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 + Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - Dave Cox at Sciex will test implement? + Dave is reviewer + Need to add two new terms - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS + Scheduled for Thursday after lunch - Other reports? ---- 5) Work on improving CV - Review action items from last teleconference 2010-07-13 + Need to update CV based on the discussion and then review + Whenever updates are made, it is automatically Next meeting: - In 3 weeks? Aug 31? + Yes *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Tuesday, August 10, 2010 1:17 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: 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 resubmitted. - 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 - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today 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 - According to folks at ISB, addition of “compensation voltage” is all that’s needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - Other items? ---- 2) MIAPE-MS revision - We have the needed 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 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 - 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 + Pierre-Alain will contact Proteo-Red again about comments + Hope that MIAPE-MS can be submitted to document process in July + Might we start a draft of MIAPE-Quant in parallel with the start of development of mzQuantML? + MIAPE-Quant will probably have different sections for each major type of quanitification ---- 3) TraML development - TraML is currently undergoing formal review in the document process - Version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 - Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - 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 ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? ---- 5) Work on improving CV - Review action items from last teleconference 2010-07-13 Next meeting: - In 3 weeks? Aug 31? |
|
From: Eric D. <ede...@sy...> - 2010-08-31 07:32:02
|
Hi everyone, sorry for the late notice. I can't make the teleconference, and I don't think we need to meet anyway, so let's cancel. As Lennart announced, the MCP paper is accepted. Final materials have been uploaded. TraML is still under review. No information back from the TraML reviewers. I will present working group activities at HUPO on the 23rd. Most action items from the previous call still need to be done. Unless pressing issues come up, let's plan on meeting again soon after HUPO. Regards, Eric _____ From: Eric Deutsch [mailto:ede...@sy...] Sent: Tuesday, August 10, 2010 10:20 AM To: Mass spectrometry standard development Cc: Eric Deutsch Subject: PSI-MSS WG call notes Present: Richard, Jim, Matt, Eric 1) mzML 1.1.0 - Manuscript has been resubmitted. - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - Eric will update the web site announcing the change and update hyperlink - Eric will update the other files - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today and compile a list of calibrants commonly used + Answer is perhaps that what the Thermo calibration compound is is not well known - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - According to folks at ISB, addition of "compensation voltage" is all that's needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - Other items? + Eric should test a recent file with multiple fragmentation types to see if they are properly labelled ---- 2) MIAPE-MS revision - We have the needed 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 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 - 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 - Pierre-Alain will contact Proteo-Red again about comments - Hope that MIAPE-MS can be submitted to document process in July - Might we start a draft of MIAPE-Quant in parallel with the start of development of mzQuantML? - MIAPE-Quant will probably have different sections for each major type of quanitification ---- 3) TraML development - TraML is currently undergoing formal review in the document process - Version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 + Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime + Matt has finished the C# bindings - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 + Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - Dave Cox at Sciex will test implement? + Dave is reviewer + Need to add two new terms - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS + Scheduled for Thursday after lunch - Other reports? ---- 5) Work on improving CV - Review action items from last teleconference 2010-07-13 + Need to update CV based on the discussion and then review + Whenever updates are made, it is automatically Next meeting: - In 3 weeks? Aug 31? + Yes From: Eric Deutsch [mailto:ede...@sy...] Sent: Tuesday, August 10, 2010 1:17 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: 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 resubmitted. - 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 - Post by Andreas Schoenegger on Jun 9 - Richard will address this by updating the schema - 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 talk to someone later today 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 - According to folks at ISB, addition of "compensation voltage" is all that's needed - Eric will try create a real example - Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? - Sometime in the future spend some time on a dozen CV terms per call to resolve them. - Other items? ---- 2) MIAPE-MS revision - We have the needed 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 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 - 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 + Pierre-Alain will contact Proteo-Red again about comments + Hope that MIAPE-MS can be submitted to document process in July + Might we start a draft of MIAPE-Quant in parallel with the start of development of mzQuantML? + MIAPE-Quant will probably have different sections for each major type of quanitification ---- 3) TraML development - TraML is currently undergoing formal review in the document process - Version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Implementations? Please update to 0.9.4 and test - Matt has implemented in ProteoWizard complete to 0.9.4 - Matt will sent out a sample file - Matt hopes to finish the C# bindings sometime - Eric will try validating with his tools - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - Jim will work to update this soon - Eric will also contact Amol to discuss TraML implementations - 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 ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Juan Pablo, Henning, and Eric - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? ---- 5) Work on improving CV - Review action items from last teleconference 2010-07-13 Next meeting: - In 3 weeks? Aug 31? |
|
From: Eric D. <ede...@sy...> - 2008-11-12 07:58:41
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Hi everyone, here are the notes I took from the call. Let me know if I've missed anything. Present: Matt, Pierre-Alain, Marc, Fredrik, Wilfred, Eric - Schema changes: no one protested, so we should go ahead and make the changes? + Yes. Marc also has some other suggested changes. + Marc has sent around a TOPP-based mzML validator and it finds several problems with the mapping file + We should run all examples through the validator and address problems + Link to this from the web site - change location of <spectrum> cvParams - scan/acquisition issue. Multiple scans inside acquisition? We need examples of what we want + Marc suggests removing scan and putting everything in acquisition + Matt and Eric should make some examples of what we want to end up with - Update rev to mzML 1.0.1 and update all documentation and examples + Yes + Make sure schemaLocation exists and is valid. It isn't now - nativeID format: Resolved. Add to documentation + Fredrik volunteers to create the CV terms for the nativeIDs - Marc has raised a number of issues to discuss. He has volunteered to maintain an open issues list + Marc will be added to SF developers and tracker admin and will set up and maintain a tracker for us - dataProcessingRef + Add a defaultDataProcessingRef attr to spectrumList and chromatogramList + Move softwareRef to processingMethod + Sematic validator should enforce that mzArray and intensityArray may not have a dataprocessingRef. This should be handled at the spectrum level. Other binaryDataArrays may have it, though. - <scanWindow> questions from Marc? + <scanWindow> should be optional. Sometimes this information will be unavailable - Removing/fixing scanning method child terms in CV + Marc has some CV issues to change. He will email out for approval + Marc needs to add some types to some CV terms that aren't there yet + Marc has a nice display of the mapping rules via a link from the TOPP validator page + Marc will create a candidate for an expanded mapping file + Make sure that the mapping file has a proper version that is publicized - Export of CV to OLS - Validator (TOPP validator and EBI validator) + validator has found some problems like cvParam deisotoping value="false" + Did we have a discussion about this in the past? For deisotoping, if the term is present, then it means it was performed. But if the term is absent, we assume that it was not performed. But it could mean unknown. While deisotoping value="false" means we know for sure it wasn't done. How to resolve? - Other + Document better when acquisitionSettings term is supported to be. + acquisitionList is too generic and maybe should be targetList. We had originally had targetList, but backed off to make it more generic. But now there is confusion between acquisition (in scan) and acquisitionList. There is no way to reference acquisitionList from acquisition. Be we never intended it this way. This is a topic for future discussion. - Next call + Same time in two weeks Nov 25 at 8am PST _____ From: Eric Deutsch [mailto:ede...@sy...] Sent: Tuesday, November 11, 2008 12:02 AM To: 'Mass spectrometry standard development' Cc: 'Eric Deutsch'; 'Natalie Tasman' Subject: PSI-MSS WG call reminder 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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