MassIVE MSV000083306

Partial Public

GNPS - Gradient benchmark dataset for ordination methods (q-Orbitrap data only)

Description

Gradient benchmarking dataset (q=Orbitrap only) . Description: Generated by the Dorrestein lab, it consists of mixtures of 4 samples prepared at different sample ratios. Method: They were analysed on the Q-Exactive and the Maxis II (qTOF), in three chromatographic conditions (C18, C18RTshift, and C18polar). METHOD Material and methods. All solvents and reactants used were LC-MS grade. Samples. Four samples were used in the gradient benchmarking dataset: - The NIST 1950 SRM human serum sample. See the following manuscript for more informations (https://pubs.acs.org/doi/suppl/10.1021/ac402503m) - Two human fecal samples collected from a male individual with a 35 days interval (Sample F1= 11-10-2013, and F2= 12-14-2013). Samples are part of the American Gut Project (https://msystems.asm.org/content/3/3/e00031-18) - A tomato seedling sample (Solanum lycopersicum) was prepared using 3 weeks post germination specimens (fresh whole seedling was used). Sample preparation. The NIST SRM 1950 sample (1mL), the two fecal samples (210 mg of fresh material each), and the tomato seedling (800 mg of fresh material) were dissolved in 1 mL of 70/30 MeOH/H2O, and homogenized in a tissue-lyser (QIAGEN) at 25 Hz for 5 min. The tubes were then centrifugated at 15,000 rpm for 15 min, and 600 uL of the supernatants was collected and load on SPE cartdriges (Oasis HLB, Hydrophilic-Lipophilic-Balance, 30 mg with particle sizes of 30 um), that were prealably activated with 100% MeOH, and 100% H2O. After loading the supernatants, 95/5 MeOH/H2O was used as wash solvent (1 mL), then the elution was carried with 70/30 MeOH/H2O (2mL), an 100% methanol (1mL). Dried extracts were resuspended in 2.5 mL of 70/30 MeOH/H2O containing 0.5 uM of amitriptiline as internal standard. These extracts were used to prepare various combination of sample ratios, such as for NIST 1950 SRM / Tomato: 100/0, 75/25, 50/50, 25/75, 0/100. See the metadata for more informations. LC-MS/MS. Samples were analyzed using ultra high performance liquid chromatography (Vanquish, Thermo Scientific) coupled to a quadrupole-Orbitrap mass spectrometer (Q Exactive, Thermo Scientific). Each sample was analyzed in triplicate, and the injection sequence was randomised. The QC mix sample was used to optimise the LC-MS/MS parameters and was injected periodically throughout the sequence. No carry over was observed. Liquid chromatography. Three different chromatographic conditions were used (named C18, C18RTshift and C18polar). Two chromatographic columns were used: the Phenomenex Kinetex C18 1.7 um (100A) 100 x 2.1 (for C18 and C18RTshift), and the Phenomenex Kinetex C18 polar 1.6 um (100A) 100 x 2.1 mm (for C18polar). Both columns were equipped with a C18 guard cartridge (Phenomenex).. The mobile phases consisted of A (100% H2O + 0.1% formic acid) and B (100% ACN + 0.1% fomic acid), and the flow rate was set to 0.5 uL/min throughout the experiment, and the column maintainted at 40C. The same chromatographic elution method was used for the C18 and C18 polar conditions: 0.00-0.25 min, 20% B; 0.25 - 4.00 min, 50% B; 4.00 - 15.00 min, 100% B; 15.00 -15.90 min, 100% B; 16.00 - 18.00 min, 20% B. Mass Spectrometry. The quadrupole-Orbitrap mass spectrometer (Q Exactive, Thermo Scientific) was fitted with an electrospray source (HESI-II) operating in positive ionisation mode. The source used the following parameters: spray voltage, +3500 V; heater temperature, 437.5°C; capillary temperature, 268.75°C; S-lens RF, 50 (arb. units); sheath gas flow rate, 52.5 (arb. units); and auxiliary gas flow rate, 13.75 (arb. units). The samples were acquired in non-targeted MS2 acquisition mode, with up to four MS2 scans of the most abundant ions per MS1 scan. The spectra were recorded from 0.48 to 17 min. The following parameters were used for full MS scan: resolution (35,000), Automatic Gain Control target (1.0 x 106), maximum injection time (125?ms), scan range (150-1500 m/z). For the data-dependent in MS2, the following parameters were used: resolution (17,500), AGC target (2.5 x 105), maximum injection time (125?ms), loop count (4), isolation window (1.5 m/z) fixed first mass (70 m/z). (70-1500 m/z) and up to four MS/MS scans of the most abundant ions per duty cycle. Higher-energy collision induced dissociation was performed with a normalized collision energy of 30 (20, 35, 50). The data-dependent settings were set as follow: minimum AGC (1.25x 104 [intensity threshold 1.0 x 105]), apex trigger 3 to 15 s, charge exclusion 3-8 and > 8, exclude isotopes (on), dynamic exclusion (14.0 s). [doi:10.25345/C5KG78] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: non-targeted LC-MS/MS ; metabolomics ; Benchmarking dataset ; Gradient benchmarking dataset

Contact

Principal Investigators:
(in alphabetical order)
Pieter C. Dorrestein, University of California at San Diego, USA
Submitting User: lfnothias
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