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Re: [Psidev-ms-dev] precursor/product/neutral loss/SRM/MSE/MS3 scans
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From: Eric D. <ede...@sy...> - 2008-12-30 00:23:48
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Hi Fredrick, thank you for the summary. This looks very good to me. Let's discuss and approve at tomorrow's call if we can get a quorum. Regarding the keyrefs, you just removed some keyrefs that were already of type ID or IDREF and therefore don't need the keyref? Thanks! Eric > -----Original Message----- > From: Fredrik Levander [mailto:Fre...@im...] > Sent: Tuesday, December 23, 2008 12:59 AM > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] precursor/product/neutral loss/SRM/MSE/MS3 > scans > > I think holidays and snow are hampering feedback, so far, but I could > summarize the proposed schema changes to make it easier to follow. > Note that it will not change anything for product scans or normal MS > scans (apart from the xmlns and version), the tiny example validates > without problem. > > Summary of changes: > > - Target namespace changed to allow schema to reside there. Version > updated to 1.1.0 > - scanList minOccurs="0" > - in spectrum, allow either precursors, product or neutraLoss element: > <xs:choice minOccurs="0" maxOccurs="1"> > <xs:element name="precursorList" > type="dx:PrecursorListType" /> > <xs:element name="product" type="dx:ProductType" /> > <xs:element name="neutralLoss" type="dx:NeutralLossType" /> > </xs:choice> > - IsolationWindowType description generalized to accomodate all types > of isolated ions. > - SelectedIonList description generalized to accomodate all types of > isolated ions > - Addition of ProductType and NeutralLossType (containing activation > and isolationWindow, no selectIonList ). > - Removed some keyrefs > > If this is OK the schema is found at: > > http://dev.thep.lu.se/fp6- > prodac/browser/trunk/mzML/scans/mzML_dev_scans.xsd > > and sample spectrum examples: > http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans > (The link was not correct in the previous post) > > Thanks, > > Fredrik > > Fredrik Levander wrote: > > Since it is quite unlikely with a sequence of isolation events within > one scan, I revised the scan examples, xsd and examples to only allow > either a precursorList, product or neutralLoss. This way there would not > be any changes to normal MS2 files. > > The updated files are found at the same URL. > > http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans > > > > These examples are really minimalistic, and probably they are not > semantically complete, but at least they validate with the xsd. > > > > thoughts? > > > > Fredrik > > > > ----- Original Message ----- > > From: Fredrik Levander <Fre...@im...> > > Date: Thursday, December 18, 2008 5:02 pm > > Subject: [Psidev-ms-dev] precursor/product/neutral loss/SRM/MSE/MS3 > scans > > > > > >> Hi All, > >> > >> To find out whether mzML is OK for various scan types, I've tried > >> to > >> write down some example scans of different types in mzML format. As > >> discussed previously, precursor and neutral loss scans didn't fit > >> well > >> into the schema. I've tried to make a minimal set of changes to the > >> schema to support different scan types. > >> I've uploaded scan examples (product / precursor / neutral loss / > >> MRM / > >> MSe / MS3) and an updated schema and sample file for discussion at: > >> http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans > >> > >> In schema terms my proposal would be to generalise precursorList by > >> renaming it to isolationList and then allow elements of types > >> 'precursor', 'product' and 'neutralLoss', that are all of the > >> 'IsolationType', which is about the same as the previous > >> 'PrecursorType'. This would make it possible to accomodate quite > >> complex > >> combinations of scans. > >> > >> Other observations: > >> - The isolation window width might not be known, should the center > >> mass > >> be given instead then? See the neutral loss example. > >> - scanList should probably be optional (as was acquisitionList and > >> scan > >> preciously) > >> - keyrefs are only necessary for spectrumId, other keys are checked > >> automatically since they are ID-IDREF. > >> > >> If anyone would like to download the files using subversion: > >> svn checkout http://dev.thep.lu.se/fp6-prodac/svn/trunk/mzML/scans > >> scans > >> Thanks, > >> > >> Fredrik > >> > >> > >> > >> -------------------------------------------------------------------- > >> ---------- > >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > >> Nevada.The future of the web can't happen without you. Join us at > >> MIX09 to help > >> pave the way to the Next Web now. Learn more and register at > >> > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.co > m/ > >> _______________________________________________ > >> Psidev-ms-dev mailing list > >> Psi...@li... > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >> > >> > > > > > > ------------------------------------------------------------------------ > ------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > > The future of the web can't happen without you. Join us at MIX09 to > help > > pave the way to the Next Web now. Learn more and register at > > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.co > m/ > > _______________________________________________ > > Psidev-ms-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > > > > -------------------------------------------------------------------------- > ---- > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
