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Re: [Psidev-ms-dev] PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT
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From: Eric D. <ede...@sy...> - 2007-06-18 07:37:10
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Hi everyone, this is a reminder of the conference call for the PSI MS = working group Tuesday, 9am PDT, 12n EDT, 5pm London, 4pm GMT. Call = information is: =20 http://www.timeanddate.com/worldclock/fixedtime.html?day=3D19&month=3D6&y= ear=3D2007&hour=3D17&min=3D0&sec=3D0&p1=3D136 =20 phone numbers are: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 =20 Agenda items are: =20 - Status and plans for: - Web site - schema - MRM support - CV - validator =20 The mzML development web page has been updated with the latest files. = You can view them at: =20 http://psidev.info/index.php?q=3Dnode/257 = <http://psidev.info/index.php?q=3Dnode/257>=20 =20 Please review the web site material and the MRM sample snippet below for = the call. =20 Regards, Eric =20 =20 =20 ________________________________ From: Eric Deutsch=20 Sent: Tuesday, June 12, 2007 9:39 AM To: 'psi...@li...' Cc: Eric Deutsch; 'Trish Whetzel'; 'Puneet Souda'; 'Juan Antonio = Vizca=EDno Gonz=E1lez' Subject: RE: PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT =20 Hi everyone, here are the notes from today's telecom. I would like to = have another call in a week to discuss the possible MRM implementation = and other items as well. I think it would also be useful to hold = another call the following week while several of us are at EBI. So the = schedule for upcoming calls is: =20 June 19: 12n EDT June 26: 12n EDT =20 Please mark your calendars. In the mean time, email discussion on the = MRM schema would be helpful! =20 Notes from today's con: =20 Present: Juan Antonio, Eric, Pete =20 - Web site Eric: The web site has been updated with the very latest files. Please = examine. Feedback is welcome. =20 - schema Eric: I added an example for encoding MRM data. The only change to the = schema was adding a spectrumType attribute which would distinguish MS1, MSn, = MRMScan, and possibly Chromatogram. Otherwise no change needed for this = implementation. There is still a list of minor mods to address, hopefully by next week. There is a meeting at EBI in two weeks. The hope is to finish the schema = then and disseminate to the community as a beta test version. =20 - MRM support Eric: Comments on the MRM implementation? Anyone? =20 - CV Eric: Latest OBO file is 1.7.4. Plans to work on this? Pete is ready to work on this. He will add terms on the list and also = write better definitions for some. Eric will add link to term tracker on web site. DONE. Pete: Individual vendors should submit their new terms to the term = tracker. Invite them after next update. =20 - Validator Lennart and Luisa will work on validator =20 =20 Action Items: - Pete has a list of things to update in the CV and will make the = updates. - Eric will send the new proposed terms for this latest rev - When Pete has finished doing any specific instrument editing, invite = all vendor to check the list and suggest changes/additions via term = tracker. =20 Thanks, Eric =20 =20 =20 ________________________________ From: Eric Deutsch=20 Sent: Tuesday, June 12, 2007 12:05 AM To: 'psi...@li...' Cc: 'Trish Whetzel'; 'Puneet Souda'; 'Juan Antonio Vizca=EDno = Gonz=E1lez'; Eric Deutsch Subject: RE: PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT =20 Hi everyone, it would be nice if everyone interested in MRM data would = have a peek at the proposed MRM implementation before the conference = call in 9 hours. =20 The high-level summary is that data are encoded something like this = (less relevant things removed and data arrays truncated to simplify the = view) [also attached as a txt file in case mailers wrap the xml too = badly]: =20 <spectrum id=3D"S19" scanNumber=3D"19" spectrumType=3D"MRMscan"> <spectrumHeader> <cvParam cvLabel=3D"PSI-MS" accession=3D"PSI-MS:1000038" = name=3D"Time" value=3D"5.890500"> <cvParam cvLabel=3D"PSI-MS" = accession=3D"PSI-MS:1000038" name=3D"Minutes" value=3D""/> </cvParam> </spectrumHeader> <binaryData precision=3D"64" compressionType=3D"none" = length=3D"3" encodedLength=3D"50"> <cvParam cvLabel=3D"PSI-MS" accession=3D"PSI-MS:9999920" = name=3D"DataArrayContentType" value=3D"Q1MassToChargeRatioArray"/> <binary>AAAAwDsGeUAAAEEnEAAAADAOg6cQA=3D=3D</binary> </binaryData> <binaryData precision=3D"64" compressionType=3D"none" = length=3D"3" encodedLength=3D"50"> <cvParam cvLabel=3D"PSI-MS" accession=3D"PSI-MS:9999921" = name=3D"DataArrayContentType" value=3D"Q3MassToChargeRatioArray"/> <binary>AAAAAAGJdeUAAAABA/nAAADAOg6cQA=3D=3D</binary> </binaryData> <binaryData precision=3D"64" compressionType=3D"none" = length=3D"3" encodedLength=3D"50"> <cvParam cvLabel=3D"PSI-MS" accession=3D"PSI-MS:9999921" = name=3D"DataArrayContentType" value=3D"IntensityArray"/> <binary>AAAAAIBJxkAAAAAAAIrXQAAAAAMysQA=3D=3D</binary> </binaryData> </spectrum> =20 <spectrum id=3D"S20" scanNumber=3D"20" spectrumType=3D"MSn"> <spectrumHeader> <cvParam cvLabel=3D"PSI-MS" accession=3D"PSI-MS:1000038" = name=3D"TimeInMinutes" value=3D"5.990230"/> <precursorList count=3D"1"> <precursor spectrumRef=3D"19"> <ionSelection> <cvParam cvLabel=3D"PSI-MS" = accession=3D"PSI-MS:9999920" name=3D"TransitionArrayElementNumber" = value=3D"2"/> <cvParam cvLabel=3D"PSI-MS" = accession=3D"PSI-MS:1000041" name=3D"ChargeState" value=3D"2"/> </ionSelection> </precursor> </precursorList> </spectrumHeader> <binaryData precision=3D"64" compressionType=3D"none" = length=3D"43" encodedLength=3D"5000"> <cvParam cvLabel=3D"PSI-MS" accession=3D"PSI-MS:9999920" = name=3D"DataArrayContentType" value=3D"MassToChargeRatioArray"/> <binary>AAAAAgKCYgEA=3D</binary> </binaryData> <binaryData precision=3D"64" compressionType=3D"none" = length=3D"43" encodedLength=3D"5000"> <cvParam cvLabel=3D"PSI-MS" accession=3D"PSI-MS:9999921" = name=3D"DataArrayContentType" value=3D"IntensityArray"/> <binary>AAAAAAD+ AAyeQAAAAAAAWIVAAAAAAABgnUA=3D</binary> </binaryData> </spectrum> =20 (excerpted from the complete: http://db.systemsbiology.net/projects/PSI/mzML/tiny2_MRM.mzML0.91.xml = <http://db.systemsbiology.net/projects/PSI/mzML/tiny2_MRM.mzML0.91.xml>=20 ) =20 There are clearly some known and obvious little issues that need to be = fixed like with the format of the CV terms, but does this capture what = we need to write out? This just handles the transition measurements and = not chromatograms. Although I don't see why we couldn't allow = chromatograms with DataArrayContentTypes of "TimeArray" and = "IntensityArray" with some CV param annotations of the appropriate q1 = and q3 values as well. =20 Opinions and discussion on this would be good. =20 Thanks, Eric =20 =20 _____________________________________________ From: Eric Deutsch=20 Sent: Sunday, June 10, 2007 11:40 PM To: 'psi...@li...' Cc: 'Trish Whetzel'; 'Puneet Souda'; 'Juan Antonio Vizca=EDno = Gonz=E1lez'; Eric Deutsch Subject: PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT =20 Hi everyone, this is a reminder of the conference call for the PSI MS = working group Tuesday, 9am PDT, 12n EDT, 5pm London, 4pm GMT. Call = information is: =20 http://www.timeanddate.com/worldclock/fixedtime.html?day=3D12&month=3D6&y= ear=3D2007&hour=3D17&min=3D0&sec=3D0&p1=3D136 = <http://www.timeanddate.com/worldclock/fixedtime.html?day=3D12&month=3D6&= year=3D2007&hour=3D17&min=3D0&sec=3D0&p1=3D136>=20 =20 phone numbers are: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 =20 Agenda items are: =20 - Status and plans for: - Web site - schema - MRM support - CV - validator =20 The mzML development web page has been updated with the latest files. = You can view them at: =20 http://psidev.info/index.php?q=3Dnode/257 = <http://psidev.info/index.php?q=3Dnode/257>=20 =20 The ABI/Sciex folks have described in a document how they would encode = MRM data, which seems to be consistent with previous thoughts. I have = updated the file tiny2_MRM.mzML0.91.xml to reflect a possible simple way = in which MRM data might be encoded (a toy example, not containing real = data). =20 If you are unable to attend but wish to pass on a comment, please email = it to me or the list. =20 Regards, Eric =20 =20 =20 |
