Re: [Psidev-ms-dev] Can mzIdentML encode a spectral library?

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

I brought this issue up in the call because I think that the "evidence" 
tag in traML is too weak to go in a standard - I was proposing that a 
better way to do it might be to refer to an mzIdentML file for a more 
complete context of the evidence.

I know very little about metabolomics, but the spectra libraries we're 
talking about are indeed proteomics-oriented. But I don't think you need 
to shut up - indeed, I think this may be another case where we can and 
should standardize within and even across domains because the 
annotations of a peptide's spectrum could be even more rich and detailed 
than that of a smaller molecule. In the spectral library domain just for 
peptides, there are at least 5 common formats already 
(http://peptide.nist.gov): MSP/ASCII, a multi-file NIST binary format, 
SpectraST, BiblioSpec, and X!Hunter. I'm sure you have a few more in the 
metabolomics domain. A lack of standards makes life so much more 
interesting, don't you think? ;)

-Matt


Steffen Neumann wrote:
> On Tue, 2009-06-30 at 08:32 -0700, Eric Deutsch wrote:
>   
>> +Can mzIdentML encode a spectral library?
>>     
>
> I am unsure whether this was discussed during the conference call, 
> or is left as an open point to the list.
>
> Anyway, I am inclined to say "no" about this,
> for two reasons: 
>
> 1) I don't know enough about analys^H^H^H^H^mzIdentML,
>    because my very brief looks made it look like proteomics-only.
>    (Or are you actually referring to a proteomics-spectral library?!
>     in that case I'll shut up and you can skip the rest of this mail.)
>
> 2) A spectral library will (at least in the future)
>    contain sets of spectra (different eV, MS1-MS^n, ...) 
>    and associated annotations, which might be as complicated 
>    as a molecule and its fragmentation brake-down products.
>    This requires a rich set of links between individual peaks 
>    and their (molecular) annotation.
>
> So for small molecules (read: metabolomics stuff) we have started
> to create mzAnnotate under the umbrella of the Metabolomics Standards
> Initiative (MSI). http://msi-workgroups.sourceforge.net/exchange-format/
>
> We have drafted some use cases, shown on
> http://sourceforge.net/apps/mediawiki/metware/index.php?title=MzAnnotate
> and prepared a converter for both the spectral library www.massbank.jp 
> and our own MassFrontier clone MetFrag, and will present these
> on the MSI mailing list soon.
>
> Yours,
> Steffen
>
>