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and MS/MS spectra were matched against HMDB, METLIN, KEGG, and the Majorbio self-compiled database (MJDB). Internal-standard peaks and known false-positive features, including noise and column-bleed signals, were removed, and redundant features were pooled. Metabolite annotations were reported with metabolite name, mass-to-charge ratio, retention time, molecular formula, database identifier, and identification confidence.MetaboLightsPublicLiquid Chromatography MS - positive - reversed-phaseLiquid Chromatography MS - negative - reversed-phaseReversed-phase liquid chromatography was performed using a Thermo Scientific UHPLC system coupled to an Orbitrap Exploris 240 mass spectrometer and an ACQUITY UPLC HSS T3 column (100 mm x 2.1 mm, 1.8 micrometre; Waters). The flow rate was 0.40 mL/min and the column temperature was 40 degrees C.Time-Resolved Microbiome–Metabolome Remodeling Reveals Biotransformation Patterns in Liquid-Fermented Dendrobium officinale Flowers.Mingyang XUANHefei University of Technologyflowermass spectrometry assayFermentation supernatants were extracted using acetonitrile:methanol (1:1, v/v) containing four internal standards, including L-2-chlorophenylalanine (0.02 mg/mL). Samples were vortexed, sonicated at 5 degrees C, incubated at -20 degrees C, centrifuged at 13000 x g, dried under nitrogen, reconstituted in acetonitrile:water (1:1, v/v), sonicated, and centrifuged before LC-MS/MS analysis.Dendrobium officinalehttps://www.ebi.ac.uk/metabolights/MTBLS15132Mingyang XUAN. Hefei University of Technology. mxuanab@connect.ust.hk.LC-MS raw data were processed using Progenesis QI for baseline filtering, peak detection, integration, retention-time correction, and peak alignment. Features detected in at least 80% of samples in any group were retained. Missing values were imputed with the minimum value, peak intensities were sum-normalized, variables with QC RSD greater than 30% were excluded, and data were log10-transformed.Fermentation timemxuanab@connect.ust.hkFermentation supernatants were collected at days 10, 20, 30, 40, 50, and 60 during a 60-day mixed-culture liquid fermentation of Dendrobium officinale flowers. Six biological replicates were collected at each time point. Supernatants were separated from fermentation pellets by centrifugation and stored at -20 degrees C until untargeted LC-MS/MS analysis. Four pooled quality-control samples were included for analytical quality control.Metabolomicspooled quality control sampleMetabolomicsuntargeted metabolomicsmixed-culture fermentationuntargeted analysisThermo Scientific UHPLC system coupled to an Orbitrap Exploris 240 mass spectrometerThermo Scientific Orbitrap Exploris 240 mass spectrometercell culture supernatantDendrobium officinaletime series designflowerpooled quality control sampleMetabolomicsuntargeted metabolomicsmixed-culture fermentationuntargeted analysisThermo Scientific UHPLC system coupled to an Orbitrap Exploris 240 mass spectrometerThermo Scientific Orbitrap Exploris 240 mass spectrometercell culture supernatantDendrobium officinaletime series designflowerMass spectrometry data were acquired on a Thermo Scientific Orbitrap Exploris 240 mass spectrometer equipped with an electrospray ionization source in separate positive and negative ion modes. The mass scan range was m/z 70-1050. Data-dependent MS/MS acquisition used stepped normalized collision energies of 20, 40, and 60.Difloxacin5-Formiminotetrahydrofolic AcidRobinetinN-[(3-Chlorophenyl)Methyl]-2-(5-Quinolin-6-Yl-1,3,4-Oxadiazol-2-Yl)AcetamideHis-Ile-IleApigenin 7-(6''-Malonylglucoside)Edulisin IThymidineMyricetin2-[[(3-Cyanopyridin-2-Yl)Amino]Carbamoyl]Benzoic AcidGilteritinibChitobioseLuteolonIndole-3-Acetylglutamic AcidCatechin 3-GlucuronideQuercetin-3,4'-Di-O-GlucosideSer-Met-Ser7-MethylinosineConcanamycin3H-Indole-3-Propanoic Acid,A-Amino-Pc(22:6/0:0)DemethylsuberosinMethylprednisolone AcetatePindoneDeoxyadenosineAnnomuricatin AMyricanene A 5-[Arabinosyl-(1->6)-Glucoside]Acuminoside6-Epi-7-Isocucurbic Acid GlucosideAsp-Phe-IleErgothioneineThr-ValAxillarinLpc(18:1)Biotin SulfoneN-(2,4-Dimethoxyphenyl)-2,5-Dimethyl-1,3-Oxazole-4-CarboxamideTaxiresinolPyropheophytin BKaempferol-3-O-Rhamnoside-7-O-RhamnosideNoreugeninN-[(2-Chlorophenyl)Methyl]-1-(3-Ethoxyquinoxalin-2-Yl)Piperidine-3-CarboxamideRamontosideGlucoheptonic AcidNorhydromorphone1-Beta-D-Arabinofuranosyl-5-Fluorocytosine3-Indolehydracrylic AcidPenciclovir4-[5-(1-Hydroxyethyl)Furan-2-Yl]-4-Oxobutanoic Acid6,8-Dihydroxy-7-Methoxy-3-Methyl-3,4-Dihydroisochromen-1-OneGln Leu LeuTetrahydrocoptisine3-DeoxyguanosineDiplosporinCichorioside KPaeonimetabolin IN-[2-(1H-Indol-3-Yl)Ethyl]FormamideCay105899-(2,5-Dimethoxyphenyl)Sulfonyl-1-Oxa-3,9-Diazaspiro[4.6]Undecan-2-OneOxypinnatanineTelotristatMinoxidil GlucuronidePa(5-Iso Pgf2Vi/2:0)SpiraeosideEremosulphoxinolide AHistidylleucinefalseTime-Resolved Microbiome–Metabolome Remodeling Reveals Biotransformation Patterns in Liquid-Fermented Dendrobium officinale FlowersThis study investigated temporal metabolomic changes during a 60-day mixed-culture liquid fermentation of Dendrobium officinale flowers. Fermentation supernatants were collected at days 10, 20, 30, 40, 50, and 60, with six biological replicates at each time point. Untargeted LC-MS/MS analysis was performed in positive and negative electrospray ionization modes using a UHPLC-Orbitrap Exploris 240 system. The deposited dataset contains raw mass spectrometry files for 36 biological samples and four pooled quality-control samples and supports the analysis of time-dependent metabolite remodeling during fermentation.2026-07-222026-07-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;PW_C000558HMDB0247453HMDB0252748HMDB0062266HMDB0000085;PW_C000058HMDB0011670HMDB0260262HMDB0029074HMDB0029782HMDB0000273HMDB0303562HMDB0014444HMDB0258751HMDB0039351HMDB0304330HMDB0254740HMDB0246793HMDB0258897HMDB0028889HMDB0252717HMDB0246269HMDB0038929HMDB0252766HMDB0001534HMDB0002755;LMPK12110001HMDB0059765HMDB0256560HMDB0303181HMDB0258794HMDB0003556HMDB0250429HMDB0301863HMDB0240434HMDB0003045HMDB0003950HMDB0041532HMDB0302057HMDB0251259HMDB0034248HMDB0002815HMDB0014004HMDB0029347HMDB0030680HMDB0256079HMDB0004818HMDB0266530HMDB0030594HMDB0037932;HMDB0257588;LMPK12112184HMDB0254661HMDB0029403HMDB0038665HMDB0000101;PW_C000068LMPK12111237LMGP01050056