psidev-ms-dev

[Psidev-ms-dev] TraML ion m/z and TraML::id attribute

[Matthew C. <mat...@va...>]

Hi,

I'm updating pwiz's TraML model to 0.9.2 and I've got some comments.

I think we need a document-level id attribute which potentially will be 
LSID just like mzML, but at least can be used to identify a document in 
some fashion.

Also, the precursor and product elements use cvParams for m/z, but just 
like mzML's selectedIon elements, we can't use the m/z unit as the main 
term for this. We could either re-use selected ion m/z (awkward?) or we 
could add a new term.

-Matt

Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute

[Eric D. <ede...@sy...>]

Thanks for working on this, Matt! Comments below. The changes will appear
in 0.9.3 to appear shortly.

> Hi,
>
> I'm updating pwiz's TraML model to 0.9.2 and I've got some comments.
>
> I think we need a document-level id attribute which potentially will be
> LSID just like mzML, but at least can be used to identify a document in
> some fashion.

Okay, added.

> Also, the precursor and product elements use cvParams for m/z, but just
> like mzML's selectedIon elements, we can't use the m/z unit as the main
> term for this. We could either re-use selected ion m/z (awkward?) or we
> could add a new term.

Sorry, I'm not understanding this issue. Can you expand on this? Currently
we have:

<Precursor>
  <CvParam cvRef="MS" accession="MS:1000040" name="m/z" value="862.9467"/>
  <CvParam cvRef="MS" accession="MS:1000041" name="charge state"
value="2"/>
</Precursor>

What's wrong with this and what are you proposing?

Thanks,
Eric


> -Matt
>
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Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute

[Matthew C. <mat...@va...>]

In our CV, the m/z term is a unit, not the name of the measurement. If 
you recall, we had the same problem in mzML. We solved it by making 
specific terms with m/z in the name, but not the whole name. So it 
should be:

<CvParam cvRef="MS" accession="xxx" name="<some kind of> m/z" value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />


-Matt

Eric Deutsch wrote:
>> Also, the precursor and product elements use cvParams for m/z, but just
>> like mzML's selectedIon elements, we can't use the m/z unit as the main
>> term for this. We could either re-use selected ion m/z (awkward?) or we
>> could add a new term.
>>     
>
> Sorry, I'm not understanding this issue. Can you expand on this? Currently
> we have:
>
> <Precursor>
>   <CvParam cvRef="MS" accession="MS:1000040" name="m/z" value="862.9467"/>
>   <CvParam cvRef="MS" accession="MS:1000041" name="charge state"
> value="2"/>
> </Precursor>
>
> What's wrong with this and what are you proposing?
>
> Thanks,
> Eric
>   
>

Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute

[Eric D. <ede...@sy...>]

Ah, I see, so you'd like to see:



<Precursor>

  <CvParam cvRef="MS" accession="MS:1000xxx" name="precursor m/z"
value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>

  <CvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>

</Precursor>

<Product>

  <CvParam cvRef="MS" accession="MS:1000xxx" name="product m/z"
value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>

  <CvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>

</Product>



Thanks,

Eric







> -----Original Message-----

> From: Matthew Chambers [mailto:mat...@va...]

> Sent: Thursday, December 17, 2009 2:28 PM

> To: Mass spectrometry standard development

> Subject: Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute

>

> In our CV, the m/z term is a unit, not the name of the measurement. If

> you recall, we had the same problem in mzML. We solved it by making

> specific terms with m/z in the name, but not the whole name. So it

> should be:

>

> <CvParam cvRef="MS" accession="xxx" name="<some kind of> m/z"

> value="862.9467" unitCvRef="MS" unitAccession="MS:1000040"

> unitName="m/z" />

>

>

> -Matt

>

> Eric Deutsch wrote:

> >> Also, the precursor and product elements use cvParams for m/z, but

> just

> >> like mzML's selectedIon elements, we can't use the m/z unit as the

> main

> >> term for this. We could either re-use selected ion m/z (awkward?) or

> we

> >> could add a new term.

> >>

> >

> > Sorry, I'm not understanding this issue. Can you expand on this?

> Currently

> > we have:

> >

> > <Precursor>

> >   <CvParam cvRef="MS" accession="MS:1000040" name="m/z"

> value="862.9467"/>

> >   <CvParam cvRef="MS" accession="MS:1000041" name="charge state"

> > value="2"/>

> > </Precursor>

> >

> > What's wrong with this and what are you proposing?

> >

> > Thanks,

> > Eric

> >

> >

>

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Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute

[Fredrik L. <Fre...@im...>]

I think it would be fine to reuse 'isolation window target m/z', 
MS:1000827, here. It is reflecting the target value for isolation, both 
for precursor and product.

Thanks

Fredrik

Eric Deutsch wrote:
>
> Ah, I see, so you'd like to see:
>
>  
>
> <Precursor>
>
>   <CvParam cvRef="MS" accession="MS:1000xxx" name="precursor m/z" 
> value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" 
> unitName="m/z"/>
>
>   <CvParam cvRef="MS" accession="MS:1000041" name="charge state" 
> value="2"/>
>
> </Precursor>
>
> <Product>
>
>   <CvParam cvRef="MS" accession="MS:1000xxx" name="product m/z" 
> value="862.9467" unitCvRef="MS" unitAccession="MS:1000040" 
> unitName="m/z"/>
>
>   <CvParam cvRef="MS" accession="MS:1000041" name="charge state" 
> value="1"/>
>
> </Product>
>
>  
>
> Thanks,
>
> Eric
>
>  
>
>  
>
>  
>
> > -----Original Message-----
>
> > From: Matthew Chambers [mailto:mat...@va... 
> <mailto:mat...@va...>]
>
> > Sent: Thursday, December 17, 2009 2:28 PM
>
> > To: Mass spectrometry standard development
>
> > Subject: Re: [Psidev-ms-dev] TraML ion m/z and TraML::id attribute
>
> >
>
> > In our CV, the m/z term is a unit, not the name of the measurement. If
>
> > you recall, we had the same problem in mzML. We solved it by making
>
> > specific terms with m/z in the name, but not the whole name. So it
>
> > should be:
>
> >
>
> > <CvParam cvRef="MS" accession="xxx" name="<some kind of> m/z"
>
> > value="862.9467" unitCvRef="MS" unitAccession="MS:1000040"
>
> > unitName="m/z" />
>
> >
>
> >
>
> > -Matt
>
> >
>
> > Eric Deutsch wrote:
>
> > >> Also, the precursor and product elements use cvParams for m/z, but
>
> > just
>
> > >> like mzML's selectedIon elements, we can't use the m/z unit as the
>
> > main
>
> > >> term for this. We could either re-use selected ion m/z (awkward?) or
>
> > we
>
> > >> could add a new term.
>
> > >>
>
> > >
>
> > > Sorry, I'm not understanding this issue. Can you expand on this?
>
> > Currently
>
> > > we have:
>
> > >
>
> > > <Precursor>
>
> > >   <CvParam cvRef="MS" accession="MS:1000040" name="m/z"
>
> > value="862.9467"/>
>
> > >   <CvParam cvRef="MS" accession="MS:1000041" name="charge state"
>
> > > value="2"/>
>
> > > </Precursor>
>
> > >
>
> > > What's wrong with this and what are you proposing?
>
> > >
>
> > > Thanks,
>
> > > Eric
>
> > >
>
> > >
>
> >
>
> > -----------------------------------------------------------------------
>
> > -------
>
> > This SF.Net email is sponsored by the Verizon Developer Community
>
> > Take advantage of Verizon's best-in-class app development support
>
> > A streamlined, 14 day to market process makes app distribution fast and
>
> > easy
>
> > Join now and get one step closer to millions of Verizon customers
>
> > http://p.sf.net/sfu/verizon-dev2dev
>
> > _______________________________________________
>
> > Psidev-ms-dev mailing list
>
> > Psi...@li... 
> <mailto:Psi...@li...>
>
> > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

[Psidev-ms-dev] traML inclusion list

[Fredrik L. <Fre...@im...>]

Hi All,

Just uploaded an initial minimalistic traML inclusion list example at:
http://dev.thep.lu.se/fp6-prodac/browser/trunk/traml/Inclusion_Yeast.traML?format=raw

Some input on the following points would be welcome:
The file is generated based on searches in X!Tandem. There is no source 
file elements yet, would it be the X!Tandem results files, the peak list 
files, or both?
The used term for target m/z is 'isolation window target m/z', ok?
I did not include any evidence tags, even if the list is based on a 
certain FDR cutoff. Would MS:1001364, 'pep:global FDR', do?

Thanks

Fredrik