Re: [Psidev-pi-dev] Added an example for N15 labelling

[Martin E. <mar...@ru...>]

Yes, agree, no chance to do it in a sensible way with mods (as I see now)...


> -----Ursprüngliche Nachricht-----
> Von: David Creasy [mailto:dc...@ma...]
> Gesendet: Thursday, August 07, 2008 4:04 PM
> An: Martin Eisenacher
> Cc: 'Angel Pizarro'; psi...@li...
> Betreff: Re: AW: [Psidev-pi-dev] Added an example for N15 labelling
> 
> Hi Martin, Angel,
> 
> The use of 15N (or other metabolic labelling) isn't really a
> modification. We'd have to duplicate every nitrogen containing
> modification in PSI-MOD - once with standard 14N and once with 15N.
> And then maybe the same for 13C...
> 
> David
> 
> 
> Martin Eisenacher wrote:
> >>> This seems to work pretty well (as expected!!)
> >>> The interesting thing is that there are two sets of residue masses, two
> >>> SpectrumIdentificationList (one for light, one for heavy) but just one
> >>> ProteinDetectionList.
> > At first glance I thought it would be better to have one residue mass list
> > and a modification for N15 (see below). But I saw it was a bad solution.
> >
> > It indeed works like you modeled it, because we don't report any masses
> > for DBSequences or Proteins.
> >
> >
> >>> And (possibly confusing at first glance!) unmodified peptides with
> >>> different masses like this:
> >>>
> >>> <Peptide id="peptide_48_1" sequenceMass="1025.481796" >
> >>>   <peptideSequence>STNLDWYK</peptideSequence>
> >>> </Peptide>
> >>>
> >>> <Peptide id="peptide_53_1" sequenceMass="1036.449188">
> >>>   <peptideSequence>STNLDWYK</peptideSequence>
> >>> </Peptide>
> >> I think this is where I come in with the mod specifications for
> >> peptide results. I'll try and add this as an example to issue 35
> > It could be possible in the current schema with the CustomModification element.
> > But that should be "extended" to report "elements" (N, C, O) instead
> > of "locations".
> > Or PSI-MOD has to include "N15 mod of amino acid X" with the respective mass
> > or delta mass, which maybe there already. But that would be quite verbose.
> >
> >   Bye
> >     Martin
> >
> 
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> David Creasy
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