Metabolites were identified based on accurate mass, retention time, and fragmentation patterns when available. Annotation was performed against public databases including KEGG (https://www.genome.jp/kegg/pathway.html), the Human Metabolome Database (https://hmdb.ca/metabolites), and LIPID MAPS (http://www.lipidmaps.org), thereby enabling functional classification and pathway enrichment analysis.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["UHPLC-MS/MS analysis was conducted by a Vanquish ultra-high-performance liquid chromatography system (Thermo Fisher Scientific, Bremen, Germany) coupled to an Orbitrap Q Exactive™ HF high-resolution mass spectrometer. Samples were separated on a Hypersil Gold C18 column (100 mm × 2.1 mm, 1.9-μm particle size) maintained at 40 °C. The mobile phase consisted of solvent A and solvent B under two ionization modes. In positive-ion mode, A was 0.1% formic acid in water and B was methanol, whereas in negative-ion mode, A was 5 mM ammonium acetate in water (pH 9.0) and B was methanol. The flow rate was set at 0.2 mL/min, and a 17-min gradient elution program was applied as follows: 0–1.5 min, 2% B; 1.5–13.5 min, linear increase from 2% to 100% B; 13.5–14.0 min, 100% B; 14.0–14.1 min, decrease to 2% B; and 14.1–17.0 min, equilibration at 2% B.
"],"publication":["Quality divergence-associated endophytic microbiome: comparative profiling unveils Sphingomonas as a pivotal driver of dihydrochalcone accumulation, growth promotion and disease suppression in Lithocarpus litseifolius (Hance) Chun."],"submitter_affiliation":["Jiangxi Agricultural University"],"submitter_name":["Wuping Yan"],"organism_part":["Fermentation"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["100 μL of culture supernatant was transferred into a 1.5-mL microcentrifuge tube and mixed with 400 μL of cold 80% methanol aqueous solution. The mixture was vortexed vigorously for 30 s to ensure complete homogenization, followed by incubation on ice for 5 min to facilitate protein precipitation. After centrifugation at 15 000 × g and 4 °C for 20 min, the supernatant was collected and diluted with mass spectrometry-grade water to adjust the final methanol concentration to 53% (v/v). The diluted sample was subjected to a second centrifugation under identical conditions (15 000 × g, 4 °C, 20 min), and the resulting supernatant was retained for UHPLC-tandem mass spectrometry (MS/MS) analysis.
"],"organism":["Sphingomonas","Quality Control"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14201"],"author":["Wuping Yan. Jiangxi Agricultural University. No.1101 Fangzhimin Avenue, Jiangxi, China. ywp1734@163.com."],"data_transformation_protocol":["Raw data were processed using Compound Discoverer 3.1 software (Thermo Fisher Scientific) for peak alignment, noise filtering, baseline correction, molecular feature detection, and isotopic pattern recognition.
"],"study_factor":["Biological replicate"],"submitter_email":["ywp1734@163.com"],"sample_collection_protocol":["The strain was cultured in LB liquid medium at 28 °C with shaking at 180 r/min for 48 h. The culture was centrifuged at 8000 r/min for 10 min, and the supernatant was filtered through a 0.22-μm membrane filter to remove bacterial cells, thereby yielding a sterile cell-free crude extract.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","Metabolomics","untargeted analysis","orbitrap","Sphingomonas","Fermentation","untargeted metabolite profiling","Quality Control"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","Metabolomics","untargeted analysis","orbitrap","Sphingomonas","Fermentation","untargeted metabolite profiling","Quality Control"],"mass_spectrometry_protocol":["Mass spectrometric detection was performed in alternating positive/negative ion-switching mode. ESI source parameters were optimized as follows: spray voltage, 3.2 kV; capillary temperature, 320 °C; sheath gas flow rate, 40 arbitrary units (arb); and auxiliary gas flow rate, 10 arb. Full-scan mass spectrometry data were acquired in the m/z range of 80–1200 with high resolution (60,000 full width at half maximum at m/z 200).
"],"metabolite_name":["metabolite_identification"],"additional_accession":[]},"is_claimable":false,"name":"Metabolomic profiling of Sphingomonas. sp (SP) fermentation broth","description":"Metabolomic profiling of the fermentation broth of Sphingomonas sp. strain SP using liquid chromatography-tandem mass spectrometry (LC-MS/MS)","dates":{"publication":"2026-04-08","submission":"2026-04-01"},"accession":"MTBLS14201","cross_references":{}}