Re: [Psidev-ms-dev] Addition of <targetList> to TraML?

[Andreas B. <be...@in...>]

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

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