OK, I have a start at the Ruby Thermo MSF library. Once it gets a little more documentation and a method to parse the peaks from the XML, I'll post the gem to rubygems.org.
For now, download and build from github. http://github.com/itmat/thermo_msf -angel On Jul 14, 1:37 pm, Matthew Chambers <[email protected]> wrote: > 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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
