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

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

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
> 

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898