MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14552/m_MTBLS14552_LC-MS_negative_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14552/m_MTBLS14552_LC-MS_positive_reverse-phase_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14552/a_MTBLS14552_LC-MS_negative_reverse-phase.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14552/s_MTBLS14552.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14552/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14552/a_MTBLS14552_LC-MS_positive_reverse-phase.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS14552Metabolite identification was performed by matching experimental m/z and MS/MS fragmentation patterns against the BiotreeDB (V3.0) and BT-Plant V1.1 libraries. Identifications were assigned according to the Metabolomics Standards Initiative (MSI) levels based on matches to authentic standards or public database entries. MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phaseChromatographic separation was performed on a Vanquish UHPLC system (Thermo Fisher Scientific) equipped with a Phenomenex Kinetex C18 column (2.1 × 100 millimeters, 2.6 micrometers). The mobile phase consisted of 0.01% acetic acid in water (Phase A) and isopropanol:acetonitrile (1:1, v/v) (Phase B). The column temperature was maintained at 25 degrees Celsius, the autosampler temperature was set to 4 degrees Celsius, and the injection volume was 2 microliters.Telomere-to-telomere genome of Stylosanthes guianensis uncovers symbiotic adaptation to phosphorus-deficient soils.Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences,Liu PandaoRootNodulemass spectrometry assayApproximately 20 ± 1 milligrams of freeze-dried plant tissue was weighed and mixed with beads. Samples were extracted with 1000 microliters of extraction solution (Methanol:Acetonitrile:Water, 2:2:1, v/v) containing deuterated internal standards. The mixture was vortexed for 30 seconds, followed by homogenization at 35 hertz for 4 minutes and sonication in a 4 degrees Celsius water bath for 5 minutes; this homogenization-sonication cycle was repeated three times. Protein precipitation was performed by incubating the samples at -40 degrees Celsius for 1 hour. Subsequently, the samples were centrifuged at 12,000 revolutions per minute (13,800 ×g) for 15 minutes at 4 degrees Celsius. An aliquot of 400 microliters of the supernatant was transferred to a protein precipitation plate and subjected to positive pressure filtration (6 pounds per square inch, 120 seconds) using a manifold device prior to LC-MS analysis.Stylosanthes guianensishttps://www.ebi.ac.uk/metabolights/MTBLS14552Liu Pandao. Chinese Academy of Tropical Agricultural Sciences. liupd@catas.cn.Raw data files were converted to the mzXML format using ProteoWizard. Feature detection, extraction, alignment, and integration were performed using an in-house R pipeline based on the XCMS package. Features were filtered based on relative standard deviation (RSD) de-noising. Missing values were imputed using half of the minimum observed value for each feature. Internal standard normalization was applied to the final dataset. Data were subsequently scaled and logarithmically transformed to minimize noise and variance. Multivariate statistical analyses, including Principal Component Analysis (PCA) and Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA), were performed using SIMCA (version 18.0.1). Model robustness was evaluated via 7-fold cross-validation and 200-time permutation testing. Variables with a Variable Importance in Projection (VIP) score > 1 and a Student's t-test p-value < 0.05 were considered statistically significantTissueliupd@catas.cnPrior to transplantation into acidic soil, 30-day-old Stylosanthes guianensis seedlings were inoculated with Bradyrhizobium (Br) strain LZ3-2. Sixty days after transplantation, root and nodule samples were collected, flash-frozen in liquid nitrogen, and stored at negative 80 degrees Celsius for subsequent untargeted metabolomic analysis.MetabolomicsThermo Scientific Vanquish UHPLC SystemMetabolomicsPlantStylosanthes guianensisRootroot noduleuntargeted analysisThermo Scientific Orbitrap Exploris 120experimental blankNoduleuntargeted metabolite profilingThermo Scientific Vanquish UHPLC SystemMetabolomicsPlantStylosanthes guianensisRootroot noduleuntargeted analysisThermo Scientific Orbitrap Exploris 120experimental blankNoduleuntargeted metabolite profilingMass spectrometric detection was carried out using an Orbitrap Exploris 120 mass spectrometer (Thermo Fisher Scientific) equipped with an electrospray ionization (ESI) source. Data acquisition was performed in both positive and negative ion modes using Information-Dependent Acquisition (IDA) controlled by Xcalibur software. The ion source parameters were set as follows: sheath gas flow rate at 50 arbitrary units, auxiliary gas flow rate at 15 arbitrary units, sweep gas flow rate at 1 arbitrary unit, capillary temperature at 320 degrees Celsius, and vaporizer temperature at 350 degrees Celsius. The spray voltage was set to 3.8 kilovolts for positive mode and -3.4 kilovolts for negative mode. Full MS resolution was set to 60,000, and MS/MS resolution was set to 15,000. Stepped normalized collision energy (SNCE) was applied at 20, 30, and 40 electron volts.falseUntargeted metabolomic analysis of Stylosanthes guianensis roots and nodules following Bradyrhizobium inoculation in acidic soilPrior to transplantation into acidic soil, 30-day-old Stylosanthes guianensis seedlings were inoculated with Bradyrhizobium (Br) strain LZ3-2. Sixty days after transplantation, root and nodule samples were collected, flash-frozen in liquid nitrogen, and stored at negative 80 degrees Celsius for subsequent untargeted metabolomic analysis.2026-05-222026-05-21MTBLS14552