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[Psidev-ms-dev] PSI-MSSWG call minutes
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From: Eric D. <eri...@gm...> - 2008-03-26 05:37:00
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Hi everyone, here are the notes I took today at the call. Thanks for participating. Present: Lennart, Darren, Matt, Josh, Eric, Parag _____ From: Eric Deutsch Sent: Monday, March 24, 2008 11:49 PM To: 'Mass spectrometry standard development' Subject: PSI-MSSWG call in 9 hr Hi everyone, the call is coming up in 9 hr. + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 During the call, let's discuss: - synching Darren's code and the xsd and example files and validator to current state Lennart will need to do some work on the validator when the schema is stable Darren will check if the xsd and his code are in synch and makes notes for - Various todo's: o JimS will provide some PDA spectrum examples Jim has examples in his head. Will send out soon. o Matt will send <chromatogram> example Everyone liked the format example. Suggested policy: individual scans always required. Full TIC is recommended. The individual SRM SICs recommended. Individual SRM TICs optional but supported. Put <chromatogramList> after <spectrumList> (so that writers can write in one pass) <chromatogram>s will be indexed. Matt will come up with an example of an index for chromatograms Matt will run a Quantum MRM file through msconvert and report results o Pierre-Alain will finish mzML <--> MIAPE mapping/checking Pierre-Alain will work on this and report results. - Figure out cvParam datatype validation plan Can we encode the xsd datatypes in the obo file? Yes, let's try. Lennart will explore this possibility, make an example, and report. Use xsd datatypes. Maybe add nonNegativeFloat, e.g. - Runup to Toledo meeting Next call on April 15, 9am PDT due to schedule conflicts on Apr 8. - Address cvParam category name issue, as described in spec doc. Do we want: A) <cvParam cvRef="MS" accession="MS:1000583" name="SRM spectrum"/> C) <cvParam cvRef="MS" accession="MS:1000583" name="SRM spectrum" categoryAccession="MS:1000035"/> (where MS:1000035="spectrum type") The category accession is not needed or used under normal circumstances by Darren's reader and presumably most readers. But it could be useful in cases where a term not known to the reader is used. Under scenario A, if the reader software predates MS:1000583, the reader will be very hard pressed to know what to do with this term. In theory, under the same scenario with option C, the reader could more easily determine what to do with this piece of information even though the exact term is unknown. Maybe "cannot determine spectrum type" should be a terminal error, while "unrecognized spectrum type" might merely be a warning. Darren and I discussed for a while at US HUPO. Let's see if we can come to a decision. Spectrum type is not a good example. Instrument model is a much better example. But even in the face of that, the general consensus is to stick with A. There is quite some dissatisfaction with adding categoryAccession and the consensus of people writing reader software is that it is not necessary. Thanks! Eric _____ From: Eric Deutsch Sent: Tuesday, March 04, 2008 10:26 AM To: 'Mass spectrometry standard development' Cc: Eric Deutsch Subject: RE: PSI-MSSWG call in 8 hr Hi everyone, here are my notes from the telecon. Thank you for your participation. Please let me know if I forgot/misunderstood anything: Meeting minutes 2008-03-04 9:00am PST Present: Darren, Jim, Matt, Lennart, Josh, Eric - Eric's most recent nativeID proposal is accepted except for the format of the value, which should be: nativeID="19" nativeID="2,6,5" nativeID="run1,3,4" nativeID=""run1,2",3,4" - possible charge state suggestion is fine with folks: - 0-1 "charge state" XOR - 2-N "possible charge state" - Come up with an example of how we want summed spectra to look: - one file that includes original scan and a summed spectrum - in old mzXML, we can have different start_scan and end_scan. How do we encode that? - defaultArrayLength proposal is fine - Jim has some examples of files with PDA data He will come up some examples of this Perhaps encoded as the MS spectrum as usual <spectrum index="27" nativeID="19"> and then another <spectrum index="28" nativeID="PDA19"> with a spectrum type "PDA spectrum" - Jim will also come up MALDI data examples for us - agreed that we rename selectionWindow to scanWindow as this is a misnomer - add optionally to <ionSelection>, all 2 new cvParams "selection window m/z lower limit" and "selection window m/z upper limit" for the *true* fragmentation selection window start and stop - agreed change acqNumber to acquisitionNumber - What to do with msLevel? agreed make it a cvParam next to spectrum type instead of a attribute of <spectrum> because for example a PDA spectrum will have no msLevel - state that index should be for seeking rather than cataloguing. So no msLevel in the index Index should be *complete* so it could be used for a list of items to seek to but should contain only identifiers, not attributes/metadata - Start a thread on this to discuss more - Matt will send <chromatogram> example since he is working on these now - Next meeting indeed March 25 as on schedule. This is *3* weeks from now, because of US HUPO - Maybe a few of us could meet and chat at US HUPO although unlikely anything official. _____ From: Eric Deutsch Sent: Tuesday, March 04, 2008 1:08 AM To: 'Mass spectrometry standard development' Cc: Eric Deutsch Subject: PSI-MSSWG call in 8 hr Hi everyone, here is a reminder of the call coming up in 8 hr. Dial-in information is: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 The agenda will be to discuss all the items that have come up recently. I list them as: - Latest nativeScanReference proposal - using defaultArrayLength attribute in <spectrum> but allow override in binaryDataArray - Allow new "possible charge state" term in <ionSelection> multiple times - Frederick suggestion that selectionWindow should really be scanWindow. selectionWindow is something different, and by the way, where is it, we really need that, too. - MS^E example - msLevel - chromatograms The schedule is still: Schedule: ----------------------- Jan 25: mzML reviews returned. Official community review complete. Feb 5: mzML telecon 9:00am PST Feb 19: mzML telecon 9:00am PST Mar 4: mzML telecon 9:00am PST Mar 17: US HUPO meeting Mar 25: mzML telecon 9:00am PST Apr 8: mzML telecon 9:00am PST Apr 23: PSI meeting in Toledo May Jun 1-5: ASMS - Must be done and advertising it here! |
