Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

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

With binary data, the same representation works for centroided and 
profile data points. I really hope you're not suggesting ASCII storage 
of profile mode data, where 9-12 bytes per X sample (12345.678901) would 
not be unusual? It's all the overhead of double precision floats (a 
constant 8 bytes) without the vastly higher dynamic range and taking 
much longer to parse.

Using mzML to store the raw data for the libraries would be a great 
improvement over the status quo (assorted custom relational databases 
and ASCII archives?). There actually would be a standard representation. 
:) Coming up with a standard representation for application-specific 
annotations would be another challenge for a possibly separate format, 
but the raw data we can already handle. And with a reasonably optimized 
representation for profile mode, storing consensus profile spectra could 
become a reasonable approach for spectral libraries. Although I do wish 
there was an XML-friendly 8-byte text encoding standard, like the yenc 
encoding used on news://alt.bin.*, which we could choose instead of 
base64 to achieve practically no encoding bloat.

-Matt


Mike Coleman wrote:
> On Thu, Jun 11, 2009 at 2:41 PM, Matthew
> Chambers<mat...@va...> wrote:
>   
>> However, NIST library folks have a quite straight-forward way to meet
>> the "human readability" requirement: XML comments. There's no reason you
>> can't put what looks like an MGF peak list in an XML comment with every
>> mzML spectrum (although presumably not profile-mode ones!).
>>     
>
> I think this would be worse than the status quo.  If this change is to
> be made, though, may I suggest that the ASCII peaks be used in the
> "real" XML and that the binary peaks go in the comments?  :-)
>
> Mike
>