Re: [Psidev-pi-dev] N15 example

[David C. <dc...@ma...>]

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
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