Re: [Psidev-ms-dev] mzML for GCxGC/MS ?

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

How different from a SCX/IEF separation is GCxGC? I know SCX can be done "online" (if I understand, 
this means the 2d separation is automatic with no manual intervention), but it usually isn't. Is 
GCxGC always online?

In mzML, we generally define a "run" as a single "injection" (except with MALDI...) so perhaps each 
2nd dimension fraction should be a separate mzML and the fraction # should be stored in the header 
(this would apply for SCX and IEF as well).

-Matt


On 3/15/2011 12:08 PM, Nils Hoffmann wrote:
> Hi Steffen, hi list!
>
> Am 15.03.11 16:19, schrieb Steffen Neumann:
>> Hi,
>>
>> Nils, do you have some (small!!) example data for GCxGC ?
> In which format? What would be the file size limit?
> Where should I upload it?
>>
>> We're wondering whether mzML could encode that with the current schema,
>> or if it has to be extended somehow.
> Well, basically, all you need is the second column modulation time (time
> interval between releases from the cryo-modulator onto the second
> column, for Leco Pegasus GCxGC-MS that is). This allows you, along with
> the scan rate, to calculate the
> number of scans for the second dimension (e.g. t_mod = 5s,
> scans_per_second:=spm =500 =>  2500 scans per modulation (mass spectra)).
> Then, with the number of scans per modulation, you can simply index
> every scan in the two-dimensional coordinate system. Basically, this
> should also work for LCxLC-(MS).
>>
>> How is netCDF handling 2D retention time ?
> Not at all, netCDF 2D from LECO ChromATof looks identical to 1D output,
> just with a very large number of scans (>1000000). We have to know the
> modulation time (duration on the second column) in advance or infer it
> from the baseline modulations.
>>
>> Yours,
>> Steffen
>>
> Yours,
> Nils
>