Hello, I'm analysing GC-MS data with MS-DIAL, but I'm unsure which data acquisition to select: DDA, AIF, or SWATH. When I analysed the data on DDA, the metabolites picked were about 2000, whereas using AIF picked 400, even though the other detecting and aligning parameters are the same for both acquisition types. The app forces you to select one of these three methods, although it doesn't seem appropriate for GC-MS data.
Thanks in advance for your insights and help.
If I am not very much mistaken is DDA, AIF, and SWATH MS/MS operations typical for HPLC-MS/MS. If You have run a classical GC-MS with electron impact ionisation on a single stage mass spectrometer this will not help much.
Thanks for your reply, Prof. Bester- that's exactly what I am getting at. I am aware that DDA, AIF, and SWATH are included in the MS-DIAL app for LC-MS-MS and GC-MS-MS, but for the classic GC-MS with a single MS stage, the app forces you to select between the three aforementioned data acquisition modes (neither of which are appropriate for GC-MS data). I am interested in how users go about processing GC-MS data with MS-DIAL?
As a long time user of MS-DIAL, I can assure you that the software does not force to choose any acquisition modality (those are for HPLC-(HR)MS). MS-DIAL clearly asks you to choose data type (GC-MS is well evidenced) and it assumes to be a hard-ionization type. You can select if data are centroided or not (for HR, but the default parameters are for low-res EI-MS). Please check carefully the parameters screens, it's quite easy.
Good work
Salvatore Chiavarini, thanks for your reply—please see the attached screenshot. When making a new project, after browsing and selecting files, in the "Raw measurement files" tab (screenshotted), either DDA, SWATH, or AIF must be selected (the default is DDA). I know that in the next tab (Measurement parameters), I can select the hard ionization/GC-MS setting.
However, I have tested that choosing DDA, SWATH, or AIF in that first tab does have a significant effect on results, hence me wondering which should be used?
Thanks for getting back to me, I appreciate it.
Dear Carla, the file selection screen gives you indeed the choice among DDA, SWATH or AIF, but if you correctly select the hard ionization/GC-MS setting that choice does not influence the results (I checked). In the old 4.x version of MS-DIAL the choice of the experiment type (GC-MS or DDA etc) came before the selection of data files and therefore the confusion was avoided. Version 5.x adds the versatility of mixing different data acquisition types for the soft-ionization techniques. Please check that you are using the exact same parameters for your tests (use the "save/load parameters" feature.
Let us know if you solved the mistery.
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