Re: [Psidev-pi-dev] N15 example

[Jones, A. <And...@li...>]

I had a vague recollection we discussed it on the call but I couldn't remember what we agreed :-)

Schema now updated with these changes, cheers Andy

> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 08 August 2008 13:41
> To: Jones, Andy
> Cc: psi...@li...
> Subject: Re: N15 example
> 
> Hi Andy,
> 
> Jones, Andy wrote:
> > Hi David,
> >
> > I'm trying to understand how best to model differential labelling e.g. the N15 file.
> I think we should view this as similar to searching for different variable mods. For
> example, if this was an ICAT, we would search for C+ICATlight and C+ICAT heavy
> within one single search.
> It's not quite the same really. The problem is that any (naturally
> occurring) modification that contains nitrogen will also have a
> different delta for that modification. And you wouldn't want to consider
> a modification with 15N masses occurring in a peptide made from 14N
> masses. However, for the sake of simplicity, I think that we can ignore
> this little detail.
> > As such, I don't think it makes sense to separate out an N15 labelling into two
> different search protocols.
> >
> Yes, (and I think that this what we agreed at the conference call).
> 
> > I think we should allow multiple mass tables within one
> SpectrumIdentificationProtocol. The MassTable also will need an id and an optional
> cv terms to explain the purpose of this particular mass table and perhaps to say if it
> is monoisotopic or average. We could then add a MassTable_ref to Peptide,
> documented saying that it is only required if more than one MassTable has been
> given.
> >
> Yes, this is what we agreed on the call:
> http://www.psidev.info/index.php?q=node/361
> > If we also have:
> >
> > <FragmentationTable>
> >           <Measure id="m_mz">
> >             <pf:cvParam cvRef="PSI-PI" accession="PI:xxxx" name="product ion
> monoisotopic m/z"/>
> >
> > To say that reported fragment ions are monoisotopic, does this also solve the
> problem if someone wants to report that precursor ions are average mass and
> product ions are monoisotopic?
> >
> Yes.
> >
> > Just to be clear however, in SpectrumIdentificationProtocol we have:
> >
> > <SpectrumIdentificationProtocol id="SIP_1"
> AnalysisSoftware_ref="AS_mascot_server">
> >       <AdditionalSearchParams>
> >
> >         ...
> >         <pf:cvParam accession="PI:00211" name="mass type setting monoisotopic"
> cvRef="PSI-PI"/>
> >
> > I didn't understand why we couldn't have two CV terms here for product and
> precursor mass setting, this is how X!Tandem sets up its searches.
> Yes, this is also what we agreed on the call - Phil's suggestion
> (although it didn't make it into the minutes).
> I've added the change request to the CV to:
> http://code.google.com/p/psi-pi/issues/detail?id=42#c2
> 
> > Was there something else that I missed here that would stop this working?
> >
> Can't think of anything (= = probably!)
> Once you've made the schema changes, I'll update the N15 example.
> 
> Thanks,
> David
> > Cheers
> > Andy
> >
> >
> >
> >
> >
> >
> 
> --
> David Creasy
> Matrix Science
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