MetaboLights

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feature tables were imported into MarVis-Suite 2.0 (Kaever et al., 2015) using MarVis-Filter. Feature intensities were log-transformed and median scaled, and differentially accumulated features were identified by one-way analysis of variance (ANOVA) with Benjamini–Hochberg false discovery rate (FDR) correction. Isotope and adduct correction was performed using a maximum of two 13C isotopes, a cosine similarity threshold ≥ 0.75, a retention time tolerance of 10 s and an m/z tolerance of 0.01 Da. Features with an adjusted p-value < 0.05 were retained for downstream analysis. Filtered features were subsequently imported into MarVis-Pathway for tentative metabolite annotation and pathway enrichment. Putative metabolite annotations were assigned by matching accurate mass and retention time information against three in-house metabolite libraries (Gamir et al., 2014), following recommendations for reporting metabolite identification confidence (Schymanski et al., 2014; Alseekh et al., 2021). KEGG was used for pathway assignment and enrichment.MetaboLightsPublicLiquid Chromatography MS - positive - reversed-phase-chromatographyLiquid Chromatography MS - negative - reverse-phaseChromatographic separation was performed using an ACQUITY UPLC I-Class system (Waters, Milford, MA, USA) equipped with a Kinetex C18 reversed-phase column (2.6 µm, 50 × 2.1 mm; Phenomenex, Torrance, CA, USA). Metabolites were separated using a water–methanol gradient containing 0.01% (v/v) formic acid at a flow rate of 0.3 mL/min. The injection volume was 5 µL.Temporal multi-omics dataset of a cucurbit–powdery mildew interaction.Alejandro Jimenez-SanchezUniversity of Malagaleafmass spectrometry assaySamples collected during the infection assay were lyophilized prior to metabolite extraction. Metabolites were extracted from 15–30 mg of lyophilized leaf powder using 1 mL of 30% (v/v) methanol containing 0.01% (v/v) formic acid. Samples were homogenized with glass beads using a TissueLyser (Qiagen, Hilden, Germany) at 30 Hz for 2 min and subsequently centrifuged at 14,000 × g for 20 min at 4 °C. The resulting supernatants were filtered through 0.22-µm regenerated cellulose syringe filters (Phenomenex, Torrance, CA, USA). Prior to LC–MS/MS analysis, extracts were diluted 1:4. Two technical replicates were prepared from each biological sample for untargeted metabolomics analysis. Solvent blanks and calibration standards (5 and 10 µg/L) were included in the analytical sequence.Cucumis melohttps://www.ebi.ac.uk/metabolights/MTBLS15447Alejandro Jiménez-Sánchez. University of Malaga. alexjisa@uma.es.Dolores Fernández-Ortuño.Álvaro Polonio. polonio@uma.es.Alejandro Pérez-García. University of Malaga. aperez@uma.es.Victoria Pastor.Raw LC–MS/MS data acquired using MassLynx v4.2 (Waters) were converted to NetCDF format using DataBridge. Data processing was performed using the xcms package (Bioconductor), including centWave peak detection, retention time correction, peak grouping and missing-value imputation. Feature intensities were normalized to sample dry weight, and the two technical replicates corresponding to each biological sample were averaged prior to downstream statistical analysis.ConditionTime pointalexjisa@uma.esFour-week-old Cucumis melo cv. Rochet plants were either mock-treated or spray-inoculated with a conidial suspension of Podosphaera xanthii (1 × 10^6 conidia/mL). Leaf samples were collected every 12 h from 12 to 144 hours post-inoculation (hpi), resulting in 12 time points. Three independent biological replicates were collected for each condition and time point, with each replicate consisting of one leaf collected from a different plant. Samples were immediately flash-frozen in liquid nitrogen, ground to a fine powder, and stored at −80 °C. Prior to metabolite extraction, samples were lyophilized.Metabolomicsultra-performance liquid chromatography-mass spectrometryMetabolomicsMulti-omics studyuntargeted analysisWaters ACQUITY UPLC I-Class SystemCucumis meloleafWaters SYNAPT G2-S HDMSexperimental sampleuntargeted metabolite profilingultra-performance liquid chromatography-mass spectrometryMetabolomicsMulti-omics studyuntargeted analysisWaters ACQUITY UPLC I-Class SystemCucumis meloleafWaters SYNAPT G2-S HDMSexperimental sampleuntargeted metabolite profilingMass spectrometric analysis was performed using a SYNAPT G2-S HDMS quadrupole time-of-flight (Q-TOF) mass spectrometer (Waters, Milford, MA, USA) coupled to an ACQUITY UPLC I-Class system. Mass spectra were acquired using electrospray ionization (ESI) in positive and negative ionization modes over an m/z range of 40–1,200. Blank injections were included between ionization modes to monitor potential carryover. Raw LC–MS/MS data were acquired using MassLynx v4.2 (Waters).falseTemporal multi-omics dataset of a cucurbit–powdery mildew interactionThis study presents a time-resolved untargeted LC–MS/MS metabolomics dataset of the interaction between melon (Cucumis melo) and the obligate biotrophic fungus Podosphaera xanthii, the causal agent of cucurbit powdery mildew. Mock-treated and inoculated plants were sampled every 12 hours from 12 to 144 hours post inoculation (12 time points), with three biological replicates per condition and two technical replicates per biological sample. Metabolites were extracted from lyophilized leaf tissue and analysed by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) in both positive and negative electrospray ionization modes. The dataset comprises raw mass spectrometry files, converted NetCDF files, sample metadata and acquisition parameters. Processed outputs include statistically significant metabolic features, putative metabolite annotations and pathway enrichment analyses, providing a resource for investigating temporal metabolic reprogramming during obligate biotrophic infection and for comparative metabolomics studies of plant–pathogen interactions.2026-09-242026-08-24MTBLS15447