I've created a similar SQLite schema (mapped with NHibernate) for IDPicker 3 and I'm storing the peak data (and most of the extra optional cvParam metadata)
in a gzipped mzML read/written by pwiz (thanks Brian Pratt!). Looks like I wasn't the first one with the idea of offloading the work of storing all those
optional spectrum attributes to embedded XML instead of a relational schema. :)
Are you going to tackle reverse engineering the ProteinPilot .group format next Angel? ;) They got quite irritated when I used their DLLs to write pepXML from
it. :(
-Matt
On 7/14/2010 12:20 PM, Angel wrote:
On Jul 14, 12:44 pm, Brian Searle<[email protected]> wrote:
Hi Angel,
This one took us a little while to figure out too-- they're just
zipped!
A HA! Before posting this message I did try a deflate using Ruby's
zlib, then unpacking the string to little endian double, but that
didn't give me any numbers that made any sense.
Based on your clue, I wrote out the string to a file, used command
line unzip on that file and it actually expanded to an XML file that
contains the spectra information. W00t! Will have to sort this out in
Ruby now.
Anyway, thanks for the tip Brian.
-angel
-Brian
On Jul 14, 7:31 am, Angel<[email protected]> wrote:
Related to this (badlt named :) )
posthttp://groups.google.com/group/spctools-discuss/browse_thread/thread/...
Thermo Proteome Discoverer uses a file format based on SQLite3. I
applaud there choice here, as it makes it insanely easy to get data
out of it, but some documentation on the format would be greatly
appreciated.
In particular, I am working on a Ruby library for reading data from
MSF file, but the Spectra table encodes the spectrum in some non-
obvious binary format. Anyone want to give me a hint as to what the
encoding is? It looks like a serialize C Struct, which I can deal with
just fine, but I need to know the fields& types to do so.
-angel
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