Lipidomics and metabolomics datasets for "Adverse effects of arsenic uptake in rice metabolome and lipidome revealed by untargeted liquid chromatography coupled to mass spectrometry (LC-MS) and regions of interest multivariate curve resolution"

Files description

Raw files for lipidomics and metabolics studies on the impact of arsenic exposure on rice growth.

File details on the worksheets lipids_files.xlsx and metabolomics_files.xlsx

Files have been organized as follows:

Lipidomics

1) Control samples: lip_controls.rar
2) Watering low As exposure: lip_water_1.rar
3) Watering high As exposure: lip_water_1000.rar
4) Soil low As exposure: lip_soil_5.rar
5) Soil high As exposure: lip_soil_50.rar
6) QC samples: lip_qcs.rar

Metabolomics (positive ionization mode)

1) Control samples: met_pos_controls.rar
2) Watering low As exposure: met_pos_water_1.rar
3) Watering high As exposure: met_pos_water_1000.rar
4) Soil low As exposure: met_pos_soil_5.rar
5) Soil high As exposure: met_pos_soil_50.rar
6) QC samples: met_pos_qcs.rar

Metabolomics (negative ionization mode)

1) Control samples: met_neg_controls.rar
2) Watering low As exposure: met_neg_water_1.rar
3) Watering high As exposure: met_neg_water_1000.rar
4) Soil low As exposure: met_neg_soil_5.rar
5) Soil high As exposure: met_neg_soil_50.rar
6) QC samples: met_neg_qcs.rar
 

Experimental details

Arsenic Exposure

Arsenic was supplied through two main routes: watering with contaminated water or soil containing arsenic. In addition, this new study includes metabolomic as well as lipidomic analysis, in order to have a more global overview of arsenic exposure.

For the watering treatment, during the first 11 days, rice was irrigated with Milli-Q water. From that day until harvesting, plants were watered with 1 and 1000 μM of As (V) for the two concentration levels of exposure, and with Milli-Q water for control samples. The lowest concentration was established at 1 μM as it is the limit of the acceptable arsenic concentration in water by European legislation. The upper concentration was set at 1000 μM, a threshold established to ensure that the experiment was performed under sub-lethal arsenic concentration for the plant, based on previous studies.

For the soil treatment, two containers were prepared with 1 kg of soil two days before planting. Soil from the container was exposed to two arsenic concentration levels (5 and 50 mg L^-1). Once sowing, rice was irrigated the whole growth period with a solution containing 0.001 μM of As (V). The lowest arsenic limit in this treatment was set at 5 mg L^-1 as a maximum value of common arsenic leaches without toxic characteristics, although background soil content of arsenic varies between one and 40 ppm according to the US food and drug administration (FDA) report. The highest arsenic limit was established to 50 mg L^-1, as a considerably high arsenic content in the soil, slightly above the maximum frequently encountered levels.

Lipidomic Analysis

The lipidomic analysis was performed using a Waters Acquity UPLC system (Waters Corporation, MA, USA), connected to a Waters LCT Premier orthogonal accelerated time of flight mass spectrometer (Waters), operated in both positive and negative electrospray (ESI) ionization modes. Full scan spectra were acquired from 50 to 1500 Da.

The chromatographic column employed was a Kinetex C8 (100 x 2.1 mm, 1.7 μm) (Phenomenex) under the following conditions (already used in [47]): temperature at 30˚C, injection volume at 10 μL, and flow rate at 0.3 mL min^-1. Mobile phases selected were (A) MeOH 1mM ammonium formate, and (B) H₂O 2mM ammonium formate, both at 0.2% formic acid. The gradient started at 80% A, increased to 90% A in 3 min, from 3 to 6 min remained at 90% A, changed to 99 % A until minute 15, remained constant 1 min, and returned to initial conditions until minute 20.

Metabolomic analysis

The metabolomic analysis was performed using a Waters Acquity UPLC system connected to a Q-Exactive (Thermo Fisher Scientific, Hemel Hempstead, UK) equipped with a quadrupole-Orbitrap mass analyzer. Electrospray (ESI) was used as an ionization source in both positive and negative ion modes. Full scan mass range was set from m/z 90 to 1000, and all ion fragmentation (AIF) was performed with normalized collision energy (NCE) of 35 eV.

The column employed was an HILIC TSK gel amide-80 column (250 x 2.0 mm i.d., 5 μm) provided by Tosoh Bioscience (Tokyo, Japan), under the following experimental conditions (already employed in [45]): flow rate at 0.15 mL min^-1, at room temperature, and 5 μL injection volume. Mobile phases were (A) AcN, and (B) 5 mM ammonium acetate, adjusted at pH 5.5 with acetic acid. The gradient employed was: starting conditions at 25% B, then increased until 30% B in 8 min; a 60% B was reached at 10 min, held for 2 min more and then back to 25% B until minute 14 min; lastly, a re-equilibration step was added and from 14 to 20 min at 25% B.

Funding: This research was funded by the Spanish Ministry of Science and Innovation (MCI, Grant CTQ2017-82598-P) and Severo Ochoa Project CEX2018-000794-S (funded by MCIN/AEI/ 10.13039/501100011033), and supported from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753). MPC was funded by a predoctoral FPU 16/02640 scholarship from the Spanish Ministry of Education and Vocational Training (MEFP).