Tomato Lipidomics Dataset (Positive/Negative ion mode)

Plant growth conditions

Tomato (Solanum lycopersicum; cv Micro Tom) plants were grown in a climate-controlled glasshouse at 24°C/18°C, day/night regime with natural light.  The fruits at the corresponding stages were collected: mature green (~30 days after pollination, DAP), breaker (~35 DAP), and mature red ripe (~45 DAP).

Lipid extraction and lipidomics analysis

For each sample, 30 mg of frozen powder was extracted with 3 mL of a pre-cooled methanol: methyl-tert-butyl ether (MTBE) mixture (1:3, v/v) containing 0.1 μg/mL glucosylceramide (d18:1/12:0) as an internal standard. The mixture was gently shaken for 30 min at 4 °C, followed by sonication for an additional 30 min. Afterward, 1.5 mL of UPLC-grade water:methanol (3:1, v/v) was added, and the samples were centrifuged to separate the phases. The upper organic phase (1.2 mL) was collected into 2 mL Eppendorf tubes. The remaining polar phase, which contained debris, was re-extracted with 0.5 mL MTBE. Organic phases were combined and dried under a stream of nitrogen. Dried lipid extracts were resuspended in 300 μL of mobile phase B (composition described below) and centrifuged at 18,000 × g for 5 min at 4 °C. For lipidomics analysis, seed samples were diluted 20-fold prior to injection.

Lipidomics analysis was performed using a Waters ACQUITY UPLC I-Class system coupled to a SYNAPT G2 HDMS mass spectrometer (Waters). Lipid separation was achieved on an ACQUITY UPLC BEH C8 column (2.1 × 100 mm, 1.7 μm particle size; Waters). The mobile phases consisted of water with 1% 1 M ammonium acetate and 0.1% acetic acid (phase A), and acetonitrile/isopropanol (7:3, v/v) containing 1% 1 M ammonium acetate and 0.1% acetic acid (phase B). The column was maintained at 40 °C, and the flow rate was 0.4 mL/min. The gradient program was as follows: 1 min at 45% A, followed by a linear gradient from 45% to 35% A over 3 min, 35% to 11% A over 8 min, and 11% to 0% A over 3 min. The column was then washed at 0% A for 4 min, returned to 45% A within 0.1 min, and re-equilibrated at 45% A for 4 min, resulting in a total run time of 22 min. Mass detection was performed using an electrospray ionization (ESI) source in both positive and negative ion modes over an m/z range of 50-1500 Da in centroid mode. Source and desolvation temperatures were set at 120 °C and 450 °C, respectively. The capillary voltage was set to 1.0 kV and the cone voltage to 40 V. Data acquisition was carried out in MSE mode, which alternates between low-energy (4 eV for both ion modes) and high-energy (10-45 eV for positive ion mode and 15-40 eV for negative ion mode) scans to capture both precursor and fragment ion spectra. Leucine-enkephalin was used as the lock-mass reference standard.