Re: [Psidev-ms-dev] PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT

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Hi everyone, here are the notes from today's 2006-06-19 telecon.

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Present: Eric Deutsch (ISB), Eva Duchoslav (Sciex), Jim Langridge =
(Waters), Ruth McNally (CESAGen), Jim Shofstahl (Thermo)

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Web site: All latest files and information are posted at:

http://psidev.info/index.php?q=3Dnode/257

No comments at this time.  Please examine the site and let Eric know if =
there are issues.

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MRM support in schema:

- Jim Shofstahl points out that for centroided mode data, the current =
implementation is good and fine, but there should the option/use case of =
profile mode MRM data where for each transition there is a m/z profile =
(like a mini MS2 scan) as well.

- Eva mentioned that in speaking with Randy, it was noted that we should =
also be able to encode the dwell time for each transition, which might =
be different for each

- Jim Langridge pointed out that it's very important to have accurate =
times for each scan. However, it was generally felt that having a time =
array might be overkill

- Jim Langridge points out that repeating the Q1 Q3 arrays over and over =
for each scan is redundant. Perhaps there could be a mechanism that =
would allow Q1 Q3s to change over time, but would not need to be =
repeated every time if the same.

- There was a discussion of chromatograms. It seemed to be agreed that =
having a mechanism to store chromatograms would be nice, but is not =
critical.  We should make sure that all kinds of chromatograms (such as =
base peak chromatograms) can be stored, not just MRM chromatograms.

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Jim Langridge (Waters) cannot be at EBI, but would very much like to =
review the result of the EBI workshop.

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After CV is revised next week, it will be sent out to all vendors and =
they will be encourage to add/suggest changes via the term tracker.

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Please let me know if I have forgotten to add anything.

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Regards,

Eric

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________________________________

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

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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:

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June 19: 12n EDT

June 26: 12n EDT

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Please mark your calendars.  In the mean time, email discussion on the =
MRM schema would be helpful!

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Notes from today's con:

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Present: Juan Antonio, Eric, Pete

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- Web site

Eric: The web site has been updated with the very latest files. Please =
examine.

Feedback is welcome.

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- 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.

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- MRM support

Eric: Comments on the MRM implementation? Anyone?

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- 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.

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- Validator

Lennart and Luisa will work on validator

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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.

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Thanks,

Eric

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________________________________

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

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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.

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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]:

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<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>

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<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>

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(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

)

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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.

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Opinions and discussion on this would be good.

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Thanks,

Eric

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_____________________________________________
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

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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:

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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

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phone numbers are:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

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Agenda items are:

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- Status and plans for:

  - Web site

  - schema

  - MRM support

  - CV

  - validator

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The mzML development web page has been updated with the latest files. =
You can view them at:

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http://psidev.info/index.php?q=3Dnode/257 =
<http://psidev.info/index.php?q=3Dnode/257>=20

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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).

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If you are unable to attend but wish to pass on a comment, please email =
it to me or the list.

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Regards,

Eric

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