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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/m_MTBLS13718_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/s_MTBLS13718.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/a_MTBLS13718_LC-MS_negative_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/H2B2.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/H2B5.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/Control3.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/W5S96.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/W5S93.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/Control4.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/HFAD1.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/Control1.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/HFAD4.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/W5S91.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/Control6.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/HFAD5.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/Control5.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/W5S94.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/HFAD2.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/H2B1.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/H2B4.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/H2B6.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/H2B3.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/HFAD3.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/Control2.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/W5S95.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/W5S92.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718/FILES/HFAD6.mzMLprimary200OKftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13718Metabolites, including bile acids, were analyzed using the QTRAP® 6500+ LC-MS/MS system equipped with an ESI Turbo Ion-Spray interface in negative ion mode. The declustering potential (DP) and collision energy (CE) for each MRM transition were further optimized to ensure the best analytical conditions.MetaboLightsPublicLiquid Chromatography MS - negative - reverse phaseThe sample extracts were analyzed using an LC-ESI-MS/MS system (UHPLC,ExionLC AD,https://sciex.com.cn/; MS,Applied Biosystems 6500 Triple Quadrupole, https://sciex.com.cn/). The analytical conditions were as follows, HPLC: column, Waters ACQUITY UPLC HSS T3 C18 (100 mm×2.1 mm i.d.,1.8 μm); solvent system, water with 0.01% acetic acid and 5 mmol/L ammonium acetate (A), acetonitrile with 0.01% acetic acid (B); The gradient was optimized at 5% to 40%B in 1 min, then increased to 50% B in 6 min, then increased to 75% B in 5 min, and then 75% to 95% in 2min, washed with 95%B for 2 min ,finaly ramped back to 5% B (16-17.5 min); flow rate, 0.35 mL/min; temperature, 40°C; injection volume: 3 μL. The effluent was alternatively connected to an ESI-triple quadrupole-linear ion trap (QTRAP)-MS.Harnessing a Germ‑Free Mouse Gut Bioreactor for Directed Evolution of Probiotics to Combat Non-Alcoholic Fatty Liver Disease.zhe hanhainan universityfecesmass spectrometrySamples (20 mg) were extracted with 495 μL methanol after the samples grinded with ball mill. 5 μL internal standard mixed solution (10 μg/mL) was added into the extract as internal standards (IS) for the quantication. Put the samples at -20°C for 10 min to precipitated protein. Then centrifugation for 10 min (12000 r/min, and 4°C), After centrifugation, supernatant through Protein Precipitation Plate for further LCMS analysis.Mus musculushttps://www.ebi.ac.uk/metabolights/MTBLS13718Zhe Han. School of Food Science and Engineering. No. 58 Renmin Avenue, Meilan District, Haikou City, Hainan Province, China. olaaaa1219@163.com.jiachao Zhang. School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou 570228, China. jiachao@hainanu.edu.cn.Data acquisition was performed using Analyst 1.6.3 software, while metabolites were quantified using Multiquant 3.0.3 software. The declustering potential (DP) and collision energy (CE) for individual MRM transitions were optimized, and specific MRM transitions were monitored according to the metabolites eluting within each time period.Dietolaaaa1219@163.comFollowing the 8-week intervention period, fresh fecal samples were collected from all mice for subsequent targeted analysis of the bile acid metabolome.MetabolomicsMulti-omics studymicrobiometargeted metabolitesMulti-omics studymicrobiometargeted metabolitesLinear ion trap (LIT) and triple quadrupole (QQQ) scans were acquired on a triple quadrupole-linear ion trap mass spectrometer (QTRAP), QTRAP® 6500+ LC-MS/MS System, equipped with an ESI Turbo Ion-Spray interface, operating in negative ion mode and controlled by Analyst 1.6.3 software (Sciex). The ESI source operation parameters were as follows: ion source, ESI-; source temperature 550 ∘C; ion spray voltage (IS) -4500 V; curtain gas (CUR) was set at 35 psi, respectively. Bile acids were analyzed using scheduled multiple reaction monitoring (MRM). falseHarnessing a Germ-Free Mouse Gut Bioreactor for Directed Evolution of Probiotics to Combat NAFLDThe data uploaded in this study were obtained from an interventional experiment in which non-alcoholic fatty liver disease (NAFLD) model mice were treated with either the original or adapted bacterial strains, followed by fecal sample collection and targeted bile acid metabolomic analysis.2026-01-202026-01-19MTBLS13718