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

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Hi Eric and Andreas,

I think the retention time list makes sense and improves both 
readability and possibilities for giving predictions for more than one 
program. For the local retention time window I think it should instead 
be two terms, representing retention time start and retention time end.  
This would be analogous to the representation of all the window 
attributes in mzML, to avoid the general confusion windows and delta 
etc.  Also, Xcalibur inclusion lists specifies start and end times 
instead of the mid time, which allows asymmetric windows.
There is a possibility that someone would like to look for the same 
peptide but at different charge states in different time windows. Maybe 
not in practice, since they should elute at the same time, but maybe if 
one of the charge states is partially overlapping another peptide. With 
the current way of specifying retention time this would not work. Would 
anyone agree upon putting the predicted retention times at the 
peptide/compound level, and the actual retention times (local) used in 
the current setup in the target list? The target list would then be 
useful as is with an identical instrumental setup, while usage with 
another gradient would imply recalculation based on the values found 
under peptide.

Thanks

Fredrik

ede...@sy... wrote:
>
>  
>
> 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.
>
>  
>
> 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... 
> <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
>
> >
>
> > Cheers,
>
> > A.
>
> >
>
> > --
>
> > 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
>
> >
>
> >
>
> >
>
> >
>
> >
>
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