Tomato Metabolomics Dataset (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).

Metabolite extraction and metabolomics analysis 

The skin, flesh, and seeds of tomato fruits at the mature green, breaker, and mature red ripe stages were manually dissected, immediately frozen in liquid nitrogen, and ground into a fine powder using an analytical mill (IKA A11 basic). For each sample, 100 mg of the frozen powder was extracted with 80% methanol:water (v/v) containing 0.1% formic acid. The mixture was briefly vortexed and sonicated for 20 min at room temperature. Extracts were then centrifuged at 14,000 × g for 15 min, and the supernatant was filtered through a 0.22 µm PTFE filter (Acrodisc® CR, 13 mm; PALL).

Metabolomics analysis was conducted using a high-resolution UPLC/qTOF system, comprising a Waters Acquity UPLC coupled to a tandem quadrupole/time-of-flight mass spectrometer (Xevo G2-S, Waters). Metabolite separation was performed using an UPLC BEH C18 column (100 × 2.1 mm, 1.7 µm, Waters Acquity). The mobile phases consisted of two solvent systems: 0.1% formic acid in acetonitrile: water (5:95, v/v; phase A) and 0.1% formic acid in acetonitrile (phase B). A linear gradient was applied as follows: 100% to 72% phase A over 22 min, 72% to 0% phase A over 14 min, held at 100% phase B for 2 min, returned to 100% phase A within 0.5 min, and conditioned at 100% phase A for 1.5 min. The flow rate was 0.3 mL/min, and the column temperature was maintained at 35 °C. 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. Instrument settings were as follows: capillary voltage, 1 kV; cone voltage, 27 V; source temperature, 140 °C; desolvation temperature, 400 °C; and desolvation gas flow, 800 L/h. Data acquisition was carried out in MSE mode, which alternates between low-energy (4 eV) and high-energy (15-45 eV) scans to capture both precursor and fragment ion spectra. Leucine-enkephalin was used as the lock-mass reference standard.

Four biological replicates (n = 4), each obtained an independent individual plant, were used for the analysis. The injection sequence was designed using RawHummus software. The sequence consists of three blank injections to stabilize the system, followed by two quality assurance (QA) injections containing a mixture of 14 standards. The study samples were subsequently analyzed in a block-randomized order. One QA sample was injected after every 10 study samples. Finally, two blank injections were run at the end of the sequence.