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From: Eric D. <ede...@sy...> - 2010-05-17 16:59:38
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Hi everyone, I now have a conflicting meeting at the usual 8am timeslot, and next week is ASMS, so I’d like to try to squeeze in the call one hour later. I hope most participants can be tolerant of this. So, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136 09:00 San Francisco 12:00 New York 15:00 London 18:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been reviewed and the comments addressed and resubmitted. - The editors have come back and asked for the inclusion of a “tangible example of an application" and then it will be acceptable for publication. Response in progress. - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink - How do we handle lock mass corrections? - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using - Jim will look at an old email and send out the information - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - Other items? ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is in preparation and will be sent out shortly ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - JuanAn maybe can’t go? - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? - Perhaps some of us try to meet at ASMS briefly? - Note that there will be a Computational Mass Spectrometry/Bioinformatics for MS meeting at ASMS - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention Center - Featuring Alexey Nesvizhskii and David L. Tabb ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 3 weeks? June 8? |
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From: Eric D. <ede...@sy...> - 2010-05-18 16:37:53
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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 - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink + Eric will update the other files - How do we handle lock mass corrections? - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using - Jim will look at an old email and send out the information + Jim will ask around at ASMS and compile a list of calibrants commonly used - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML + Eric will talk to Chris at ISB - Other items? + Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? + Sometime in the future spend some time on a dozen terms per call to resolve them. ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard + ProteoWizard implementation is complete to 0.9.4 + Matt has sent out a sample file + Matt hopes to finish the C# bindings this week + Eric will try validating with his tools - Andreas will implement in OpenMS and update on-line validator + Sadly Andreas has perished in a car accident and is no longer with us - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? + Eric will follow up with David - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is in preparation and will be sent out shortly ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - JuanAn maybe can’t go? - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? - Perhaps some of us try to meet at ASMS briefly? - Note that there will be a Computational Mass Spectrometry/Bioinformatics for MS meeting at ASMS - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention Center - Featuring Alexey Nesvizhskii and David L. Tabb ---- 5) Working with ASMS on controlled vocabulary - no update + Matt suggested slowly working through purgatory at these calls. Eric will prep. Next meeting: - In 3 weeks? June 8? Regular time + agreed *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, May 17, 2010 9:59 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call reminder <1 hr time shift!> Hi everyone, I now have a conflicting meeting at the usual 8am timeslot, and next week is ASMS, so I’d like to try to squeeze in the call one hour later. I hope most participants can be tolerant of this. So, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136 09:00 San Francisco 12:00 New York 17:00 London 18:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been reviewed and the comments addressed and resubmitted. - The editors have come back and asked for the inclusion of a “tangible example of an application" and then it will be acceptable for publication. Response in progress. - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink - How do we handle lock mass corrections? - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using - Jim will look at an old email and send out the information - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - Other items? ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is in preparation and will be sent out shortly ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - JuanAn maybe can’t go? - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? - Perhaps some of us try to meet at ASMS briefly? - Note that there will be a Computational Mass Spectrometry/Bioinformatics for MS meeting at ASMS - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention Center - Featuring Alexey Nesvizhskii and David L. Tabb ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 3 weeks? June 8? |
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From: Eric D. <ede...@sy...> - 2010-06-07 17:34:12
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Hi everyone, due a schedule change, I am unable to make it to tomorrow’s PSI-MSS WG call. Let’s meet a week later instead, Jun 15 8am PDT, unless this causes some serious problem? Thanks, Eric *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Tuesday, May 18, 2010 9:38 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call notes Present: Matt, Richard, Jim, Eric Agenda: 1) mzML 1.1.0 - Manuscript has been reviewed and the comments addressed and resubmitted. - The editors have come back and asked for the inclusion of a “tangible example of an application" and then it will be acceptable for publication. Response in progress. + Richard suggests a jzmzml as an application + Matt suggests quantification, wiff files, spectrum annotation - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink + Eric will update the other files - How do we handle lock mass corrections? - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using - Jim will look at an old email and send out the information + Jim will ask around at ASMS and compile a list of calibrants commonly used - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML + Eric will talk to Chris at ISB - Other items? + Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? + Sometime in the future spend some time on a dozen terms per call to resolve them. ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard + ProteoWizard implementation is complete to 0.9.4 + Matt has sent out a sample file + Matt hopes to finish the C# bindings this week + Eric will try validating with his tools - Andreas will implement in OpenMS and update on-line validator + Sadly Andreas has perished in a car accident and is no longer with us - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? + Eric will follow up with David - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is in preparation and will be sent out shortly ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - JuanAn maybe can’t go? - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? - Perhaps some of us try to meet at ASMS briefly? - Note that there will be a Computational Mass Spectrometry/Bioinformatics for MS meeting at ASMS - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention Center - Featuring Alexey Nesvizhskii and David L. Tabb ---- 5) Working with ASMS on controlled vocabulary - no update + Matt suggested slowly working through purgatory at these calls. Eric will prep. Next meeting: - In 3 weeks? June 8? Regular time + agreed *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, May 17, 2010 9:59 AM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call reminder <1 hr time shift!> Hi everyone, I now have a conflicting meeting at the usual 8am timeslot, and next week is ASMS, so I’d like to try to squeeze in the call one hour later. I hope most participants can be tolerant of this. So, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136 09:00 San Francisco 12:00 New York 17:00 London 18:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been reviewed and the comments addressed and resubmitted. - The editors have come back and asked for the inclusion of a “tangible example of an application" and then it will be acceptable for publication. Response in progress. - Matt has released and posted the updated 1.1.1 version of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” to disallow other creative values - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - New schema is posted on the web. The tiny file has been updated. - Eric will update the web site announcing the change and update hyperlink - How do we handle lock mass corrections? - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Formiate; others? - Jim will find out what Thermo is using - Jim will look at an old email and send out the information - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - Other items? ---- 2) MIAPE-MS revision - Document is ready to be submitted, but.. - We need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Pierre-Alain has received an example from Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - Pierre-Alain is looking through PRIDE to find a good example. - The last example would be a MIAPE compliant mzML document - Looking in Peptidome might be an alternative for finding a nicely annotated dataset - Waiting to sync with MIAPE-MSI as well - Keep working on our documents and when we’re ready, see if we should wait - We also need to coordinate the creation of MIAPE-Quant - When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is in preparation and will be sent out shortly ---- 4) PSI session at World HUPO in Sydney - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. - JuanAn maybe can’t go? - Eric will present on the work of the group: mzML 1.1, TraML x.x, MIAPE-MS - Abstract is accepted - Other reports? - Perhaps some of us try to meet at ASMS briefly? - Note that there will be a Computational Mass Spectrometry/Bioinformatics for MS meeting at ASMS - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace Convention Center - Featuring Alexey Nesvizhskii and David L. Tabb ---- 5) Working with ASMS on controlled vocabulary - no update Next meeting: - In 3 weeks? June 8? |
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From: Matthew C. <mat...@va...> - 2010-06-15 15:04:24
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Do we have the call now? -Matt On 6/7/2010 12:33 PM, Eric Deutsch wrote: > > Hi everyone, due a schedule change, I am unable to make it to > tomorrow’s PSI-MSS WG call. Let’s meet a week later instead, Jun 15 > 8am PDT, unless this causes some serious problem? > > Thanks, > > Eric > > *From:* Eric Deutsch [mailto:ede...@sy... > <mailto:ede...@sy...>] > *Sent:* Tuesday, May 18, 2010 9:38 AM > *To:* Mass spectrometry standard development > *Cc:* Eric Deutsch > *Subject:* PSI-MSS WG call notes > > Present: Matt, Richard, Jim, Eric > > Agenda: > > 1) mzML 1.1.0 > > - Manuscript has been reviewed and the comments addressed and resubmitted. > > - The editors have come back and asked for the inclusion of a > “tangible example of an application" and then it will be acceptable > for publication. Response in progress. > > + Richard suggests a jzmzml as an application > > + Matt suggests quantification, wiff files, spectrum annotation > > - Matt has released and posted the updated 1.1.1 version of > indexedmzML schema: <indexList> name attribute will be enumerated to > “spectrum” or “chromatogram” to disallow other creative values > > - Matt will update the example files to reference mzML 1.1.0 but > indexedmzML 1.1.1 > > - New schema is posted on the web. The tiny file has been updated. > > - Eric will update the web site announcing the change and update hyperlink > > + Eric will update the other files > > - How do we handle lock mass corrections? > > - We should assemble list of calibrants and make them specific terms > > - Bruker uses Lithium Formiate; others? > > - Jim will find out what Thermo is using > > - Jim will look at an old email and send out the information > > + Jim will ask around at ASMS and compile a list of calibrants > commonly used > > - Matt will contact David Anderson and Mike Ashton and ask about a > date in lieu of checksum > > - Need to test FAIMS support in mzML > > + Eric will talk to Chris at ISB > > - Other items? > > + Have the questions from Steffen on Apr 7 and Apr 8 all been resolved? > > + Sometime in the future spend some time on a dozen terms per call to > resolve them. > > ---- > > 2) MIAPE-MS revision > > - Document is ready to be submitted, but.. > > - We need to have 3 examples to go along with a document submission > > - Until we provide the examples, it is not officially in the document > process > > - We can use the sample MIAPE-compliant mzML file > > - Pierre-Alain will contact Juan-Pablo to see if he has some suitable > examples in Proteo-Red > > - Pierre-Alain has received an example from Proteo-Red > > - Richard will look into PRIDE to see if there may be a good example there > > - Pierre-Alain is looking through PRIDE to find a good example. > > - The last example would be a MIAPE compliant mzML document > > - Looking in Peptidome might be an alternative for finding a nicely > annotated dataset > > - Waiting to sync with MIAPE-MSI as well > > - Keep working on our documents and when we’re ready, see if we should > wait > > - We also need to coordinate the creation of MIAPE-Quant > > - When officially in the process, send out submitted document to > journal editors and everyone else to get the word out > > ---- > > 3) TraML development > > - New version 0.9.4 released and is available at > http://www.psidev.info/index.php?q=node/405 > > - Specification document is updated. Please examine. Is it ready for > submission? > > http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc > > - Implementations? Please update to 0.9.4 and test > > - Matt will implement in ProteoWizard > > + ProteoWizard implementation is complete to 0.9.4 > > + Matt has sent out a sample file > > + Matt hopes to finish the C# bindings this week > > + Eric will try validating with his tools > > - Andreas will implement in OpenMS and update on-line validator > > + Sadly Andreas has perished in a car accident and is no longer with us > > - ISB implementation in ATAQS nearly done > > - Jim has an implementation but just will need to update to 0.9.4 > > - David Cox at Sciex will test implement? > > + Eric will follow up with David > > - Are we ready to update validator page?: > http://www.psidev.info/index.php?q=node/304 > > - Manuscript is in preparation and will be sent out shortly > > ---- > > 4) PSI session at World HUPO in Sydney > > - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. > > - JuanAn maybe can’t go? > > - Eric will present on the work of the group: mzML 1.1, TraML x.x, > MIAPE-MS > > - Abstract is accepted > > - Other reports? > > - Perhaps some of us try to meet at ASMS briefly? > > - Note that there will be a Computational Mass > Spectrometry/Bioinformatics for MS meeting at ASMS > > - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace > Convention Center > > - Featuring Alexey Nesvizhskii and David L. Tabb > > ---- > > 5) Working with ASMS on controlled vocabulary > > - no update > > + Matt suggested slowly working through purgatory at these calls. Eric > will prep. > > Next meeting: > > - In 3 weeks? June 8? Regular time > > + agreed > > *From:* Eric Deutsch [mailto:ede...@sy... > <mailto:ede...@sy...>] > *Sent:* Monday, May 17, 2010 9:59 AM > *To:* Mass spectrometry standard development > *Cc:* Eric Deutsch > *Subject:* PSI-MSS WG call reminder <1 hr time shift!> > > Hi everyone, I now have a conflicting meeting at the usual 8am > timeslot, and next week is ASMS, so I’d like to try to squeeze in the > call one hour later. I hope most participants can be tolerant of this. > > So, the next PSI Mass Spectrometry Standards Working Group call will > be Tuesday 9am PDT: > > http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136 > <http://www.timeanddate.com/worldclock/fixedtime.html?day=18&month=5&year=2010&hour=17&min=0&sec=0&p1=136> > > 09:00 San Francisco > > 12:00 New York > > 17:00 London > > 18:00 Geneva > > + Germany: 08001012079 > > + Switzerland: 0800000860 > > + UK: 08081095644 > > + USA: 1-866-314-3683 > > Generic international: +44 2083222500 (UK number) > > access code: 297427 # > > Agenda: > > 1) mzML 1.1.0 > > - Manuscript has been reviewed and the comments addressed and resubmitted. > > - The editors have come back and asked for the inclusion of a > “tangible example of an application" and then it will be acceptable > for publication. Response in progress. > > - Matt has released and posted the updated 1.1.1 version of > indexedmzML schema: <indexList> name attribute will be enumerated to > “spectrum” or “chromatogram” to disallow other creative values > > - Matt will update the example files to reference mzML 1.1.0 but > indexedmzML 1.1.1 > > - New schema is posted on the web. The tiny file has been updated. > > - Eric will update the web site announcing the change and update hyperlink > > - How do we handle lock mass corrections? > > - We should assemble list of calibrants and make them specific terms > > - Bruker uses Lithium Formiate; others? > > - Jim will find out what Thermo is using > > - Jim will look at an old email and send out the information > > - Matt will contact David Anderson and Mike Ashton and ask about a > date in lieu of checksum > > - Need to test FAIMS support in mzML > > - Other items? > > ---- > > 2) MIAPE-MS revision > > - Document is ready to be submitted, but.. > > - We need to have 3 examples to go along with a document submission > > - Until we provide the examples, it is not officially in the document > process > > - We can use the sample MIAPE-compliant mzML file > > - Pierre-Alain will contact Juan-Pablo to see if he has some suitable > examples in Proteo-Red > > - Pierre-Alain has received an example from Proteo-Red > > - Richard will look into PRIDE to see if there may be a good example there > > - Pierre-Alain is looking through PRIDE to find a good example. > > - The last example would be a MIAPE compliant mzML document > > - Looking in Peptidome might be an alternative for finding a nicely > annotated dataset > > - Waiting to sync with MIAPE-MSI as well > > - Keep working on our documents and when we’re ready, see if we should > wait > > - We also need to coordinate the creation of MIAPE-Quant > > - When officially in the process, send out submitted document to > journal editors and everyone else to get the word out > > ---- > > 3) TraML development > > - New version 0.9.4 released and is available at > http://www.psidev.info/index.php?q=node/405 > > - Specification document is updated. Please examine. Is it ready for > submission? > > http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc > > - Implementations? Please update to 0.9.4 and test > > - Matt will implement in ProteoWizard > > - Andreas will implement in OpenMS and update on-line validator > > - ISB implementation in ATAQS nearly done > > - Jim has an implementation but just will need to update to 0.9.4 > > - David Cox at Sciex will test implement? > > - Are we ready to update validator page?: > http://www.psidev.info/index.php?q=node/304 > > - Manuscript is in preparation and will be sent out shortly > > ---- > > 4) PSI session at World HUPO in Sydney > > - PSI will have a session. Presenters will be Eric, Juan Antonio, Henning. > > - JuanAn maybe can’t go? > > - Eric will present on the work of the group: mzML 1.1, TraML x.x, > MIAPE-MS > > - Abstract is accepted > > - Other reports? > > - Perhaps some of us try to meet at ASMS briefly? > > - Note that there will be a Computational Mass > Spectrometry/Bioinformatics for MS meeting at ASMS > > - Wednesday, May 26th, 2010, 05:45-07:00pm Hall 2, Salt Palace > Convention Center > > - Featuring Alexey Nesvizhskii and David L. Tabb > > ---- > > 5) Working with ASMS on controlled vocabulary > > - no update > > Next meeting: > > - In 3 weeks? June 8? > > > ------------------------------------------------------------------------------ > 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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