MetaboLights

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annotation was performed using Progenesis QI 2.3 by matching the experimental LC/MS spectra and accurate mass measurements against multiple reference databases, including the Human Metabolome Database, LipidMaps, METLIN, and self built databases (Shanghai LuMing Biotech) containing over 2000 compounds (e.g., organic acids, sugars, lipids, flavonoids, terpenoids) built from authentic standards. A mass accuracy tolerance of ±5 ppm was applied during database matching, and retention time alignment was used to further confirm annotation confidence. Functional classification and pathway mapping were subsequently carried out using KEGG compound IDs.MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phaseChromatographic separation was performed on a Thermo Scientific Dionex UltiMate 3000 UHPLC system coupled with a Thermo Scientific Q-Exactive Plus Orbitrap mass spectrometer. The column was a Waters ACQUITY UPLC HSS T3 column (100 mm × 2.1 mm, 1.8 μm). The column temperature was maintained at 45 °C. The mobile phases consisted of (A) water with 0.1% formic acid and (B) acetonitrile with 0.1% formic acid. The flow rate was 0.35 mL/min, and the injection volume was 2 μL. The gradient elution program was as follows: 0–2 min, 5% B; 2–4 min, 5–30% B; 4–8 min, 30–50% B; 8–10 min, 50–80% B; 10–14 min, 80–100% B; 14–15 min, 100% B; 15–15.1 min, 100–5% B; 15.1–16 min, 5% B.Tree species identity is associated with rhizosphere microbiome assembly via root metabolite-mediated feedbacks in subtropical forests.Lishui Vocational and Technical CollegeYuemei ZhangMixedmass spectrometry assayFor metabolite extraction, 1 g of rhizosphere soil was mixed with 10 μL of internal standard (2-chloro-l-phenylalanine in methanol, 0.3 mg/mL) and 1 mL of methanol/water (1:1, v/v). The mixture was frozen at –20 °C for 2 min, then grinded at 60 Hz for 2 min and centrifuged at 7700 rpm for 10 min at 4 °C. 2.5 mL of supernatant in a brown and glass vial was dried in a freeze concentration centrifugal dryer. The dried residue was reconstituted in 400 μL of methanol/water (1:4, v/v), vortexed, and centrifuged again at 12000 rpm for 10 min at 4 °C. The final supernatant was filtered through a 0.22 μm membrane prior to LC/MS analysis. Quality control (QC) samples were prepared by pooling equal volumes of all individual sample extracts. Procedural blanks (extraction solvent without soil) were also processed alongside the samples to monitor background contamination. The internal standard was used to correct for variations in extraction efficiency and instrument response.Liquidambar formosanacontrolPinus massonianahttps://www.ebi.ac.uk/metabolights/MTBLS15227Yuemei Zhang. Lishui Vocational and Technical College. zymei23394@njfu.edu.cn.The acquired LC MS raw data were analyzed by the progqenesis QI software (Waters Corporation Milford, USA) using the following parameters. Precusor tolerance was set 5 ppm, fragment tolerance was set 10 ppm, and retention time (RT) tolerance was set 0.02 min. Internal standard detection parameters were deselected for peak RT alignment, isotopic peaks were excluded for analysis, and noise elimination level was set at 10.00 minimum intensity was set to 15 % of base peak intensity The Excel file was obtained with three dimension data sets including m/z, peak RT and peak intensities, and RT-m/z pairs were used as the identifier for each ion. The resulting matrix was further reduced by removing any peaks with missing value (ion intensity = 0) in more than 50 % samples. The internal standard was used for data QC (reproductility).Rhizosphere typezymei23394@njfu.edu.cnRhizosphere soil samples were collected from four distinct vegetation types. Six biological replicates were randomly selected from each type, yielding a total of 24 samples. All samples were collected at the same developmental stage to minimize temporal variation. Immediately after collection, the samples were frozen in liquid nitrogen and subsequently stored at –80 °C until metabolite extraction. No additional chemical treatments were applied to the samples prior to storage.Metabolomicsultra-performance liquid chromatography-mass spectrometryMetabolomicsuntargeted analysiscontrolmzmineThermo Scientific Dionex Ultimate 3000 HPLC systemThermo Scientific Q Exactive Plusexperimental sampleuntargeted metabolite profilingMixedLiquidambar formosanaThermo Scientific Dionex Ultimate 3000 UHPLC systemPinus massonianaultra-performance liquid chromatography-mass spectrometryMetabolomicsuntargeted analysiscontrolmzmineThermo Scientific Dionex Ultimate 3000 HPLC systemThermo Scientific Q Exactive Plusexperimental sampleuntargeted metabolite profilingMixedLiquidambar formosanaThermo Scientific Dionex Ultimate 3000 UHPLC systemPinus massonianaMass spectrometry detection was performed on a Thermo Scientific Q Exactive Plus with a heated electrospray ionization (ESI) source. An ACQUITY UPLC HSS T3 (100 mm×2.1 mm, 1.8 um) were employed in both positive and negative modes. The binary gradient elution system consisted of (A) water (containing 0.1% formic acid, v/v) and (B) acetonitrile (containing 0.1% formic acid, v/v) and separation was achieved using the following gradient 0 min, 5% B; 2 min, 20% B; 4 min, 25% B; 9 min, 60% B; 14 min, 100% B; 18 min, 100% B; 18.1 min, 5% B and 19.5 min, 5% B. The flow rate was 0.4 mL/min and column temperature was 45 °C. All the samples were kept at 4 °C during the analysis. The injection volume was 2 μL. The mass range was from m/z 100 to 1200. The resolution was set at 70000 for the full MS scans and 35000 for HCD MS/MS scans. The Collision energy was set at 10, 20 and 40 eV. The mass spectrometer operated as follows spray voltage, 3800 V (+) and 3000 V (-) sheath gas flow rate, 35 arbitrary units; auxiliary gas flow rate, 8 arbitrary units capillary temperature, 320 °C. The QCs were injected at regular intervals (every 10 samples) throughout the analytical run to provide a set of data from which repeatability can be assessed.falseTree species identity is associated with rhizosphere microbiome assembly via root metabolite-mediated feedbacks in subtropical forestsThis experiment investigates the rhizosphere metabolome of two subtropical tree species (Pinus massoniana and Liquidambar formosana) grown in pure and mixed forest stands. Rhizosphere soil samples were collected from each forest type, and root-associated metabolites were extracted and analyzed using untargeted liquid chromatography–mass spectrometry (LC-MS) in both positive and negative ionization modes. The primary objective is to characterize the metabolic profiles associated with different tree species and neighbor interactions, and to provide a comprehensive metabolite dataset that can be linked to microbial community composition and soil nutrient dynamics. The dataset includes raw LC-MS files, feature tables, and annotated putative metabolite identifications.2026-08-022026-08-02MTBLS15227