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Re: [Psidev-ms-dev] Addition of <targetList> to TraML?
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From: Eric D. <ede...@sy...> - 2009-10-27 08:01:21
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Hi Andreas, attached is an updated example and xsd. Please look these over and let us know what you think. And let's discuss at the call. Thanks! Eric > -----Original Message----- > From: Andreas Bertsch [mailto:be...@in...] > Sent: Sunday, October 25, 2009 11:28 PM > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] Addition of <targetList> to TraML? > > Hi Eric, > > > Hi Andreas, can you provide a move complete definition of the > > retention time window? I wouldn't think that a "window" is a > > property of a peptide. It is rather a tolerance within which one > > wants to look for a peptide? And it depends on your gradient, of > > course. The window you use might well differ for a 30 min vs 90 mins > > gradient, right? > > > > Maybe we would be better off putting the different retention times > > in separated elements under a retentionTimeList. This might provide > > some more specificity and flexibility with only minor additional > > verbosity. > Yes, separating retention time is a good idea. I also agree with the > idea of Fredrik to use two terms to specify the retention time window. > Maybe, we should document the way how asymmetric RT windows are > handled to create lists, if only one symmetric RT window is allowed > (like in QTrap 4000). > > Maybe it is also a good idea to have a mandatory CV term that > describes the source of the RT, which gives a hint about the > reliability if more than one is present. E.g. database, prediction > software, experimental... > > Can you update the schema first, before we update the examples? > Writing the files without a schema to validate, is like blind flying ;). > > Cheers, > A. > > > > > So instead of what we have now: > > > > <retentionTime predictedRetentionTimeSoftwareRef="SSRCalc3.0"> > > <cvParam cvRef="MS" accession="MS:1000895" name="local > > retention time" value="40.02" unitCvRef="UO" unitAccession="UO: > > 0000031" unitName="minute"/> > > <cvParam cvRef="MS" accession="MS:1000896" name="normalized> > > retention time" value="38.43" unitCvRef="UO" unitAccession="UO: > > 0000031" unitName="minute"/> > > <cvParam cvRef="MS" accession="MS:1000902" name="H-PINS > > retention time normalization standard"/> > > <cvParam cvRef="MS" accession="MS:1000897" name="predicted > > retention time" value="44.07" unitCvRef="UO" unitAccession="UO: > > 0000031" unitName="minute"/> > > </retentionTime> > > > > We might do: > > > > <retentionTimeList> > > <retentionTime softwareRef="Skyline0.5">> > > <cvParam cvRef="MS" accession="MS:1000895" name="local > > retention time" value="40.02" unitCvRef="UO" unitAccession="UO: > > 0000031" unitName="minute"/> > > <cvParam cvRef="MS" accession="MS:1000XXX" name="retention time > > window" value="3.0" unitCvRef="UO" unitAccession="UO:0000031" > > unitName="minute"/> > > </retentionTime> > > <retentionTime> > > <cvParam cvRef="MS" accession="MS:1000896" name="normalized > > retention time" value="38.43" unitCvRef="UO" unitAccession="UO: > > 0000031" unitName="minute"/> > > <cvParam cvRef="MS" accession="MS:1000902" name="H-PINS > > retention time normalization standard"/> > > </retentionTime> > > <retentionTime softwareRef="SSRCalc3.0"> > > <cvParam cvRef="MS" accession="MS:1000897" name="predicted > > retention time" value="44.07" unitCvRef="UO" unitAccession="UO: > > 0000031" unitName="minute"/> > > </retentionTime> > > > > How does this strike y'all? > > > > Thanks, > > Eric > > > > > > > > > > > > > -----Original Message----- > > > From: Andreas Bertsch [mailto:be...@in...] > > > Sent: Wednesday, October 07, 2009 1:50 AM > > > To: Mass spectrometry standard development > > > Subject: Re: [Psidev-ms-dev] Addition of <targetList> to TraML? > > > > > > Hi Pierre-Alain, > > > > > > > I beleive that Retention time window restriction is also > > applicable > > > > here by adding a corresponding cvParam, right? > > > The retention time information is stored at the compound and peptide > > > entries, just the same mechanism as used in transition sections. > > Here > > > a snippet from the toy example: > > > > > > ..... > > > <peptide id="ADTHFLLNIYDQLR-M1" proteinRef="Q12149"> > > > <cvParam cvRef="MS" accession="MS:1000888" name="unmodified > > > peptide sequence" value="ADTHFLLNIYDQLR"/> > > > <cvParam cvRef="MS" accession="MS:1000889" name="modified > > > peptide sequence" value="ADTHFLLNIYDQLR[162.10111]"/> > > > ..... > > > <cvParam cvRef="MS" accession="MS:1001117" name="theoretical > > > mass" value="1189.22" unitCvRef="UO" unitAccession="UO:0000221" > > > unitName="dalton"/> > > > <retentionTime > > predictedRetentionTimeSoftwareRef="SSRCalc3.0"> > > > <cvParam cvRef="MS" accession="MS:1000895" name="local > > > retention time" value="40.02" unitCvRef="UO" unitAccession="UO: > > > 0000031" unitName="minute"/> > > > <cvParam cvRef="MS" accession="MS:1000896" name="normalized > > > retention time" value="38.43" unitCvRef="UO" unitAccession="UO: > > > 0000031" unitName="minute"/> > > > <cvParam cvRef="MS" accession="MS:1000902" name="H-PINS > > > retention time normalization standard"/> > > > <cvParam cvRef="MS" accession="MS:1000897" name="predicted > > > retention time" value="44.07" unitCvRef="UO" unitAccession="UO: > > > 0000031" unitName="minute"/> > > > </retentionTime> > > > .... > > > </peptide> > > > .... > > > > > > > > > So far there is now CV term to restrict the retention time window. > > > However, we should add one. > > > > > > [Term] > > > id: MS:XXXXXXXX > > > name: retention time window > > > def: "Retention time window of e.g. a compound" [PSI:PI] > > > xref: value-type:xsd\:double "The allowed value-type for this CV > > term." > > > relationship: has_units UO:0000010 ! second > > > relationship: has_units UO:0000031 ! minute > > > > > > I think it should be allowed as an attribute of a peptide or > > compound, > > > but also as a global setting, e.g. some instruments allow only the > > > global setting of a retention time window > > -- > Div. for Simulation of Biological Systems, WSI, University of Tuebingen > Room C322, Sand 14, 72076 Tuebingen, Germany > phone: +49-7071-29-70461 fax: +49-7071-29-5152 > http://www-bs.informatik.uni-tuebingen.de > > > > > > -------------------------------------------------------------------------- > ---- > Come build with us! 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