psidev-pi-dev

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

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

Hi,

I've added an example N15 Mascot search to:
http://code.google.com/p/psi-pi/source/browse/#svn/trunk/examples/schema_usecase_examples/working29July

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.

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>

Any comments welcomed...

-- 
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

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

[Angel P. <an...@ma...>]

On Thu, Jul 31, 2008 at 8:45 AM, David Creasy <dc...@ma...> wrote:
> Hi,
>
> I've added an example N15 Mascot search to:
> http://code.google.com/p/psi-pi/source/browse/#svn/trunk/examples/schema_usecase_examples/working29July
>
> 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.
>
> 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
-angel

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

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

> > 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

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

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
> >
> 
> --
> 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