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

[Steffen N. <sne...@ip...>]

Hi,

On Sun, 2011-03-20 at 19:00 +0100, Oliver Kohlbacher wrote:
...
> Conceptually, I would consider those just a single {L|G}C-MS run.
> Information on how the 1D RT should be mapped to 2D coordinates
> should be provided in addition to that. We could basically 
> store a relation assigning each scan two or more retention 
> coordinates (retention times or an index for the primary separation,
> which would also make it comparable to offline fractionation).

I now got my hands on some example data from Nils Hoffmann 
http://www.cebitec.uni-bielefeld.de/~hoffmann/files/GCxGC-MS-LECO.tar.bz2
which I converted with the OpenMS-1.8 FileConverter 
http://msbi.ipb-halle.de/~sneumann/GCxGC_leco.mzML.bz2

1) OpenMS is already able to extract some information from the netCDF 
   where we lack the proper cvTerms. I would suggest 
   (also see separate mail on "inlet attribute")

[Term]
id: MS:1000XXX
name: inlet temperature 
def: "Inlet temperature." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
is_a: MS:1000XXX ! inlet attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius

[Term] 
id: MS:1000XXX
name: source temperature 
def: "Source temperature ... ." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000012 ! kelvin
relationship: has_units UO:0000027 ! degree celsius

2a) For GCxGC, we need to specify the 2D coordinate / time system. 
   I would minimally suggest a new "run attribute":

[Term]
id: MS:1000XXX
name: modulation time
def: "The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second
dimension chromatogram, i.e., the time between two successive injections
into the second column." [not PSI:MS ?]
xref: value-type:xsd\:string "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

   BTW: how do we "cite" the definition ? I it took from 
   http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429
   There are tons more terms in this paper.

2b) Alternatively/additionally, we'd need to be able to add 
    several dimensions to the scan attribute "elution time". 

     MS:1000503 ! scan attribute
     + MS:1000826 ! elution time 
       + MS:1000XXX ! first column elution time (def: Retention time of a
                                   peak in the first dimension of a
                                   comprehensive two-dimensional system)
       + MS:1000XXX ! second column elution time (def: ... second ...)
       + MS:1000XXX ! third column elution time 
       ...
       + MS:1000XXX ! seventh column elution time (you get the idea ...)

     Does anyone have a better idea ? Please ? Or is this reasonable 
     with current (and anticipated) seperation techniques ?
     The paper above also lists GCϫGCϫGC, LC–GCϫGC or ...
     I don't like the ordering in the name, but anything else would 
     rather be in the scope of sepML, and we still need to reference 
     several elution times.

Usually, the 2a) modulation time is the "run attribute" that is programmed 
into the GCxGC-MS system when you run your samples. The actual elution
times for each scan could be 2b) adjusted / corrected if there are any 
shifts/deviations (for whatever reason) within the run.

Thoughts ?

Yours,
Steffen

Just for reference, here is the netCDF metadata from above file(s):

netcdf header information GCxGC {
dimensions:
...
	point_number = UNLIMITED ; // (43969157 currently)
	scan_number = 100001 ;
variables:
...
// global attributes:
		:netcdf_file_date_time_stamp = "20090325161325+0100" ;
		:experiment_date_time_stamp = "20090306200015+0100" ;
		:experiment_type = "Centroided Mass Spectrum" ;
		:test_separation_type = "Gas-Liquid Chromatography" ;
		:test_ms_inlet = "Capillary Direct" ;
		:test_ms_inlet_temperature = 275.f ;
		:test_ionization_mode = "Electron Impact" ;
		:test_ionization_polarity = "Positive Polarity" ;
		:test_source_temperature = 200.f ;
		:test_accelerating_potential = -600.f ;
		:test_detector_type = "Electron Multiplier" ;
		:test_detector_potential = -1600.f ;
		:test_resolution_type = "Constant Resolution" ;
		:test_scan_function = "Mass Scan" ;
		:test_scan_direction = "Up" ;
		:test_scan_law = "Linear" ;
		:test_scan_time = 0.0002f ;
...
}


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
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                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409