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Sample Set Information

ID SE126
Title Test dataset for MS-DIAL 2.0 and MS-FINDER 2.0
Description Three validation kits are prepared for the evaluation of MS-DIAL 2.0 and MS-FINDER 2.0.

(1) The validation of MS-DIAL chromatogram deconvolution for GC/MS data was performed by six raw data files from five major MS vendors.
(2) Software comparison of MS-DIAL against other alternative programs was performed by four raw data files.
(3) Software comparison of MS-FINDER against other alternative programs was performed by five EI-MS spectra.

The raw files except for Bruker Daltonics and Thermo Fisher Scientific (because of their contracts) can be downloaded.

Authors Zijuan Lai, Hiroshi Tsugawa, Gert Wohlgemuth, Matthew Mueller, Yuxuan Zheng, Atsushi Ogiwara, Sajjan Mehta, John Meissen, Kohei Takeuchi, Tobias Kind, Peter Beal, Masanori Arita, Oliver Fiehn
Reference Lai et al. (2018) Nature Methods Jan;15(1):53-56. doi: 10.1038/nmeth.4512

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The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Sample Information

Title Chlamydomonas reinhardtii
Organism - Scientific Name Chlamydomonas reinhardtii
Organism - ID NCBI taxonomy 3055
Compound - ID
Compound - Source
Sample Preparation Details ID

Analytical Method Information

Title Agilent GC-QTOF(MS)
Method Details ID MS3
Sample Amount 1 μL

Analytical Method Details Information

Title Agilent GC-QTOF(MS)
Instrument Agilent 7890A GC system (Agilent Technologies) , Agilent 7200 accurate mass Q-TOF mass spectrometer (Agilent Technologies)
Instrument Type
Ionization EI, CI
Ion Mode Positive
Description Extraction procedures

All metabolite extraction procedures were kept on ice, and the quantities for sample aliquots were 25 μL for blood plasma, 5 x 10^6 for cells, 5 mg for tissues, and 2 mL for algae cultures. Metabolites were extracted with 1,000 μL of degassed acetonitrile:isopropanol:water (3:3:2, v/v/v) and then homogenized, centrifuged, decanted, and evaporated. Extracts were cleaned with 500 μL of degassed acetonitrile:water (1:1, v/v) to remove triglycerides and membrane lipids, and evaporated again. For GC-MS analysis, internal standard C8–C30 fatty acid methyl esters were added to determine the retention index. The dried samples were derivatized with 10 μL of methoxyamine hydrochloride (or ethoxyamine hydrochloride) in pyridine and subsequently by 90 μL of MSTFA (or MSTFA-d9) for trimethylsilylation of acidic protons.

Briefly, for GC-MS analysis, we used an Agilent 7890A GC system (Agilent Technologies) and an Agilent 7200 accurate mass Q-TOF mass spectrometer (Agilent Technologies) with the transfer line temperature maintained at 290 °C. Chromatography was done on an Rxi-5Sil MS column (30 × 0.25 mm, 0.25 μm; Restek) with helium (99.999%; Airgas) at a constant flow of 1 mL/min. The GC temperature program was set as follows: initial temperature of 60 °C with a hold time of 1 min, a temperature ramp of 10 °C/min to 325 °C, and a final hold time of 9.5 min at 325 °C. The injection volume was 1 μL in splitless mode at 250 °C. Mass spectra were acquired from m/z 50 to m/z 800 at a 5-Hz scan rate and 750-V detector voltage in both electron ionization (EI) mode and chemical ionization (CI) mode. Other data acquisition parameters were as follows: EI ion source temperature, 230 °C; EI electron energy, 70 eV; CI ion source temperature, 300 °C; CI electron energy, 135 eV; CI gas flow rate, 20%; CI gas, methane (99.999%; Airgas).

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