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

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Hi Eric,

should we also define something like an inlet attribute (referenced by 
inlet temperature)?

[Term]
id: MS:1002039
name: inlet attribute
def: "Inlet properties that are associated with a value." [PSI:MS]
is_a: MS:1000547 ! object attribute

Best,
Gerhard

Am 24.05.2012 01:17, schrieb Eric Deutsch:
> Hi everyone, I think this issue fell by the wayside a while back. I spoke
> with Nils Hoffmann as ASMS and he urged that we get these in the CV so he
> can use them. So I propose that we add the following terms.
>
> Unless there are objections, would you add these at the next interval,
> Gerhard?
>
> Thanks!
> Eric
>
> [Term]
> id: MS:1000XXX
> name: inlet temperaturedef:
> "The temperature of the inlet of a mass spectrometer." [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: "The temperature of the source of a mass spectrometer." [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
>
>   [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."
> [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429]
> 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
>
>
>
>> -----Original Message-----
>> From: Steffen Neumann [mailto:sne...@ip...]
>> Sent: Friday, May 27, 2011 12:46 AM
>> To: Mass spectrometry standard development
>> Subject: Re: [Psidev-ms-dev] mzML for GCxGC/MS ?
>>
>> 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+M
>> atters/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
>> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>>                                    +49 (0) 345 5582 - 0
>> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
>>
>>
>>
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-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
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