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

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

Sorry, I meant 1st dimension. E.g. SCX fractions, IEF strips. If each fraction only lasts a few 
minutes, it might make more sense to keep in one mzML. But in that case, the 1st dimension fraction 
identifier would need to be a spectrum property. Looked at another way, do the scan numbers, or 
whatever the instrument uses, reset when moving to the next fraction?

-Matt


On 3/15/2011 3:54 PM, Neumann, Steffen wrote:
> Hi,
>
> no, I think the 2nd dimension is in such a rapid succession (few seconds!),
> that a single metabolite elutes across several of those,
> and hence it makes no sense to split into multiple files.
>
> Yours,
> Steffen
>
> ________________________________________
> From: Matthew Chambers [mat...@gm...]
> Sent: 15 March 2011 21:25
> To: psi...@li...
> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS ?
>
> You propose a<run>  cvParam, but there is only one run per mzML. So you are agreeing with me that
> each 2nd dimension fraction would be a separate mzML? Constructing the 2d x vs. y would require
> reading from multiple mzMLs then.
>
> -Matt
>
>
> On 3/15/2011 2:59 PM, Neumann, Steffen wrote:
>> Hi,
>>
>> Yes, GCxGC is (almost ?) always online. Here is an image:
>> http://www.purdue.edu/discoverypark/bioscience/facilities/mpf/capabilities.php
>>
>> if I get it orrectly, the Y axis is the "fast" column (think seconds),
>> the X axis the "slow" column (order of minutes). Each Pixel would be a TIC,
>> with a full spectrum "behind" it. (Or did I mix the axes up ?)
>>
>> There is also some course material, including GCxGC/TOF-MS at p27
>> http://depts.washington.edu/chemcrs/bulkdisk/chem429A_spr07/notes_Comprehensive2D.pdf
>>
>> So as Nils confirmed, mzML is technically capable of carrying GCxGC data
>> as a (large) number of spectra.
>>
>> However, I'd like to have (at least a rudimentary) encoding for the GCxGC settings,
>> so that images such as the one above can be created. This would also be
>> required for 2D peak picking (or alignment). No need to encode all sorts
>> of GC column information, that might go into sepML or whatever.
>>
>> Following Nils, I'd suggest something like
>>
>> [Term]
>> id: MS:1000XXX
>> name: second column modulation time
>> def: "The time of ..." [PSI:MS]
>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>> is_a: MS:1000857 ! run attribute
>> relationship: has_units UO:0000010 ! second
>> relationship: has_units UO:0000031 ! minute
>>
>> as a<cvParam>   for the<run>. Any software ignoring this 2D nature
>> would simply see a (very) strange pattern of spectra.
>>
>> Thoughts ? Does anyone have contact with sbd. at Leco ?
>> Which are the other major players with GCxGC ?
>>
>> Yours,
>> Steffen