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Re: [Psidev-ms-dev] mzML for GCxGC/MS
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From: pierre-alain b. <pie...@is...> - 2012-09-28 07:15:38
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Hi Steven, On 27.09.2012 21:58, Robles, Steve wrote: > > Hi Nils, Pierre-Alain, Matt and all, > > Thanks for the feedback. It seems like everyone agrees that there > should be an elution time for each column. > > Pierre-Alain's suggestion for MS:100826 definition change to "The time > of elution from all used chromatographic columns (one or more) in the > chromatographic separation step, relative to the start of the > chromatography." sounds good to me. But I'm not sure what the third > global term for the function would be. Are you suggesting a term for > the run element that indicates if it GCxGC, LCxLC ? Or something about > the modulation period? > I'm referring to a term describing the function that implements the relationship between elution time and modulation time (you have given two examples below). This might be useful or not. mzML describes MS acquisition parameters, and we could as well describe this as part of the run gobal params. If this sounds a useful term, I let you propose what is the most appropriate. Cheers Pierre-Alain > Thanks again, > > *Steven Robles *| Software design engineer > ste...@le... > > Description: LECOLOGO3.png* > **Delivering the Right Results* | 3000 Lakeview Ave. | St. Joseph | MI > | 49085 > > Visit us online at www.leco.com <http://www.leco.com/>|Register to > receive e-news & updates > <http://visitor.r20.constantcontact.com/manage/optin/ea?v=001Ii8Y_QGk40pWa6GMO_HQlr4axErCoyfnebuJojN8G0hnJbPCz9PezRG9EoMLF3XTe8r9jqIrcaw%3D> > > *From:*Nils Hoffmann [mailto:nil...@ce...] > *Sent:* Thursday, September 27, 2012 2:32 PM > *To:* Robles, Steve > *Cc:* psi...@li... > *Subject:* Re: [Psidev-ms-dev] mzML for GCxGC/MS > > Hi Steve, > as one of the original requestors of the modulation_time term, I > totally agree with your option nr. 2 to handle more possible > use-cases. We simply opted for the simpler option first since we did > not have reference data available for other modulation regimes. Fyi, > there was a thread started by Steve Reichenbach recently on 2D LC-MS > that circled around non-uniform modulation schemes and which might > also be of interest here. > > Nils Hoffmann > > -- > Nils Hoffmann phone: +49-521-106-4342 > Bielefeld University room: U10-144 > Faculty of Technology, Genome Informatics > P.O. Box 10 01 31 > 33501 Bielefeld, Germany > > > "Robles, Steve" <Ste...@le... > <mailto:Ste...@le...>> schrieb: > > Hi everyone, > > We would like to export our two-dimensional GCxGC-MS data to mzML and > include the first and second column elution times. > > There was a thread in the psidev-ms-dev email archive that covered > this topic and resulted in the modulation time term being added to CV > https://sourceforge.net/mailarchive/forum.php?thread_name=assp.7128de5073.1306482337.4700.551.camel%40paddy&forum_name=psidev-ms-dev. > > [Term] > > id: MS:1002042 > > 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 > > The modulation time allows the elution time from the first and second > column to be calculated. However, our instrument allows the modulation > time to vary over the course of a single run so that there can be more > than one value for this field. Examples can be found on page 4 of this > site > http://www.leco.com/products/sep_sci/pegasus_4d/pdf/SEP%20SCI%20PEGASUS%204D%20GCxGC-TOFMS%20209-183.pdf > and > http://www.labmate-online.com/articles/chromatography/1/leco_corporation/analysis_of_samples_from_the_gulf_of_mexico_oil_spill_by_gcxgc-tofms_-_leco_corporation/815/ > > To fully describe the data we would not only need a term for each > modulation time but also a matching field that describes the scan or > elution time that the modulation time is effective. For example > consider the following table: > > Time from injection (s) Modulation Time (s) > > 0 0 > > 50 4 > > 130 5 > > 430 ` 6 > > Here acquisition starts at 50 seconds from injection. Spectra acquired > from 50 s to anything less than 130 s will have a modulation time of 4 > s; spectra acquired from 130 s to anything less than 430 s will have a > modulation time of 5 s; and anything acquired at 430 s or after will > have a modulation time of 6 s. > > The second and first column elution time can be described by: > > t2 = (t -- ti) % mi > > t1 = t -- t2 > > Where: > > t1 is the first column elution time > > t2 is the second column elution time > > t is the time from injection > > ti is the greatest modulation start time from injection that is less > than or equal to t > > mi is the modulation time that goes with ti > > So for example a spectrum at t = 136 would have a second column > elution time of 1 and a first column elution time of 135. > > The only way we could represent this data with the current schema and > CV would be to break the sample into three different files, each with > a different modulation time. However we would prefer to keep the > sample in a single file. > > We can think of a few ways to handle this problem. > > 1)The first would be to include the list of modulation times and have > the software that is reading the file calculate the first and second > column elution times. This could be implemented in at least a couple > of different ways. > > a.A new list object added to the run element. Each item in the list > would require two cvParams, one for the modulation start time (a new > term?) and a modulation time. > > b.Instead of a list element, create a specific series of elements for > both the modulation time and modulation start time (i.e. modulation > time 1, modulation start time 1, modulation time 2, modulation start > time 2, ...). > > 2)Another approach would be to create two new terms "first column > elution time" and "second column elution time", and add these to scan > elements. There was a suggestion like this in the original thread that > wasn't implemented. > > 3)Just create a " second column elution time term" and store the first > column term in the elution time MS:1000826. > > The first approach will not increase the file size as much as the > others but requires more changes to the schema or CV. It also requires > the importing application to calculate the elution times. The second > approach doesn't require the importing application to know how to > determine the elution times. It only requires a couple of new CV terms > but will increase the file size the most. The third option has the > drawback that the it will usually produce multiple spectra with the > same elution time MS:1000826 which may cause trouble for some > applications. > > We prefer the second option since its straight-forward and it avoids > the possibility of misinterpretation by the application reading the > file. Does anyone have any other suggestions? > > It might also be a good idea to update the definition of MS:1000826 -- > elution time from "The time of elution from a chromatographic column, > relative to the start of the chromatography."" to "The time of elution > from all chromatographic columns, relative to the start of the > chromatography." > > Sorry we missed the original thread when this topic came up; we've > been following Psidev-ms-vocab and not Psidev-ms-dev. We're glad to > see an effort is being made to support comprehensive separation > techniques with mzML. > > Thank you, > > *Steven Robles *| Software design engineer > ste...@le... <mailto:ste...@le...> > > Description: LECOLOGO3.png* > **Delivering the Right Results* | 3000 Lakeview Ave. | St. Joseph | MI > | 49085 > > Visit us online at www.leco.com <http://www.leco.com/>|Register to > receive e-news & updates > <http://visitor.r20.constantcontact.com/manage/optin/ea?v=001Ii8Y_QGk40pWa6GMO_HQlr4axErCoyfnebuJojN8G0hnJbPCz9PezRG9EoMLF3XTe8r9jqIrcaw%3D> > > ------------------------------------------------------------------------ > > > *LECO Corporation Notice:*This communication may contain > confidential information intended for the named recipient(s) > only. If you received this by mistake, please destroy it and > notify us of the error. Thank you. > > ------------------------------------------------------------------------ > > > *LECO Corporation Notice:* This communication may contain > confidential information intended for the named recipient(s) > only. If you received this by mistake, please destroy it and > notify us of the error. Thank you. > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://ad.doubleclick.net/clk;258768047;13503038;j? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
