Using Compound Discoverer 3.3, MS information was matched, searched, and annotated against BMDB (BGI Metabolome Database), mzCloud, and the ChemSpider online database to obtain metabolite identifications. The identification results were integrated with the peak-area data to generate the final data matrix.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reversed-phase-chromatography","Liquid Chromatography MS - alternating - reverse-phase"],"chromatography_protocol":["Chromatographic separation was performed using an ACQUITY UPLC I-Class system (Waters, USA) equipped with a BEH C18 column (1.7 μm, 2.1 × 100 mm; Waters, USA). In positive-ion mode, mobile phase A was water containing 0.1% formic acid and mobile phase B was methanol containing 0.1% formic acid. In negative-ion mode, mobile phase A was water containing 10 mM ammonium formate and mobile phase B was 95% methanol containing 10 mM ammonium formate. The gradient was as follows: 0–1 min, 2% B; 1–6 min, 2%–98% B; 6–8 min, 98% B; 8–8.1 min, 98%–2% B; and 8.1–10 min, 2% B. The flow rate was 0.35 mL/min, the column temperature was 45 °C, and the injection volume was 5 μL.
Equal-volume aliquots of the bacterial culture samples and BHI blank controls were used for metabolite extraction. Each aliquot was supplemented with 10 μL of internal standard 1 and 800 μL of methanol/acetonitrile/water (2:2:1, v/v/v), followed by thorough mixing for 5 min. Samples were incubated at −20 °C for 2 h and centrifuged at 25,000 × g for 15 min at 4 °C. A 600-μL aliquot of the supernatant was transferred to a new tube and freeze-dried. The dried extract was reconstituted in 250 μL of 50% aqueous methanol, mixed until completely dissolved, and centrifuged at 25,000 × g for 15 min at 4 °C. The resulting supernatant was transferred to an autosampler vial. A pooled quality-control sample was prepared by combining 30 μL from each processed sample.
The raw mass spectrometry files were imported into Compound Discoverer 3.3 (Thermo Fisher Scientific, USA) for peak detection and peak alignment. The parameters were set as follows: precursor-ion mass tolerance, <5 ppm; fragment-ion mass tolerance, <10 ppm; and retention-time tolerance, <0.2 min. Processing generated a data matrix containing metabolite-feature peak areas, which was subsequently used for downstream data curation and statistical analyses.
"],"study_factor":["Culture condition"],"submitter_email":["wangh823@mail2.sysu.edu.cn"],"sample_collection_protocol":["Veillonella parvula was inoculated into brain heart infusion (BHI) medium and cultured for 1 week under strictly anaerobic conditions. Uninoculated BHI medium served as the blank control and was processed in parallel with the bacterial cultures. At the end of cultivation, the bacterial culture samples and BHI blank controls were aliquoted into centrifuge tubes and stored immediately at −80 °C until metabolomic analysis to minimize degradation or alteration of microbial metabolites during storage.
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","BHI broth","bacterial culture supernatant","untargeted analysis","Waters ACQUITY UPLC I-Class System","culture medium","High-resolution mass spectrometry","Thermo Scientific Orbitrap Fusion Lumos","Veillonella parvula","culture supernatant","uninoculated BHI medium","Untargeted metabolomics"],"curator_keywords":["Metabolomics","BHI broth","bacterial culture supernatant","untargeted analysis","Waters ACQUITY UPLC I-Class System","culture medium","High-resolution mass spectrometry","Thermo Scientific Orbitrap Fusion Lumos","Veillonella parvula","culture supernatant","uninoculated BHI medium","Untargeted metabolomics"],"mass_spectrometry_protocol":["MS1 and MS2 data were acquired using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, USA). The scan ranges were m/z 70–1050 in positive-ion mode and m/z 92–1050 in negative-ion mode. MS1 resolution was 120,000, the AGC target was 3 × 10^6, and the maximum injection time was 100 ms. The three most intense precursor ions were selected for fragmentation. MS2 resolution was 30,000, the AGC target was 1 × 10^5, the maximum injection time was 50 ms, and stepped normalized collision energies of 20, 40, and 60 eV were used. ESI source parameters were as follows: sheath gas flow rate, 40; auxiliary gas flow rate, 10; spray voltage, 3.20 kV in both positive- and negative-ion modes; capillary temperature, 320 °C; and auxiliary gas heater temperature, 350 °C.