MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/m_MTBLS12276_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/a_MTBLS12276_LC-MS_positive_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/a_MTBLS12276_LC-MS_negative_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/s_MTBLS12276.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/DSS3_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/VP3_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/VP2_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/DSS2_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/DSS2_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/VP1_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/QC02_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/DSS4_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/VP4_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/DSS4_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/QC02_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/VP1_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/VP4_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/VP3_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/DSS1_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/VP2_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/DSS1_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/QC03_NEG.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/DSS3_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/QC03_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/POS/QC01_POS.mzXMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276/FILES/NEG/QC01_NEG.mzXMLprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12276In this study, metabolites were identified and annotated using a combination of advanced computational pipelines and well-established reference databases. Raw data acquired from mass spectrometry (MS) analyses were processed using the XCMS software suite, which enabled feature detection, alignment and peak integration. To identify metabolites, the extracted features were compared against several comprehensive metabolite reference databases, including the Human Metabolome Database (HMDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the METLIN database. The identification process included matching accurate mass, retention time and fragmentation patterns, with a focus on ensuring a high level of confidence in metabolite identification. Metabolites that could not be fully identified based on these criteria were annotated based on known chemical structures and fragmentation patterns from the databases. The data analysis pipeline also incorporated MetaboAnalyst for further statistical analysis and visualization, ensuring robust interpretation of the metabolic profiles. This multi-step approach, integrating high-quality reference databases with reliable software tools, ensures that the metabolite annotations are accurate and reproducible.MetaboLightsPublicLiquid Chromatography MS - negative - reverse phaseLiquid Chromatography MS - positive - reverse phaseLC-MS/MS analyses were performed using an UHPLC system (Vanquish, Thermo Fisher Scientific) with a Phenomenex Kinetex C18 (2.1 mm x 100 mm, 2.6 μm) coupled to Orbitrap Exploris 120 mass spectrometer (Orbitrap MS, Thermo). The mobile phase A: 0.01% acetic acid in water; mobile phase B: IPA:ACN (1:1, v/v). The auto-sampler temperature was 4 °C and the injection volume was 2 μL. The Orbitrap Exploris 120 mass spectrometer was used for its ability to acquire MS/MS spectra on information-dependent acquisition (IDA) mode in the control of the acquisition software (Xcalibur, Thermo). In this mode, the acquisition software continuously evaluates the full scan MS spectrum. The ESI source conditions were set as following: sheath gas flow rate as 50 Arb, Aux gas flow rate as 15 Arb, capillary temperature 320 °C, full MS resolution as 60000, MS/MS resolution as 15000, collision energy: SNCE 20/30/40, spray voltage as 3.8 kV (positive) or -3.4 kV (negative), respectively.Ectopic intestinal colonization by an oral commensal promotes C. difficile infection in Crohn’s disease.Ziyu YangShanghai Jiao Tong UniversityStandard QCfecesmass spectrometryThe fecal samples (100 mg ± 1 mg) were taken, mixed with beads and 500 μL of extraction solution (MeOH:ACN:H2O, 2:2:1, v/v). The extraction solution contains deuterated internal standards. The mixed solutions were vortexed for 30 s.Mus musculusStandard QChttps://www.ebi.ac.uk/metabolights/MTBLS12276Yang Ziyu. Shanghai Jiao Tong University. Shanghai Jiao Tong University. yyyzzzyyy@sjtu.edu.cn. 028-13262906006.The raw data were converted to the mzXML format using ProteoWizard and processed with an in-house program, which was developed using R and based on XCMS, for peak detection, extraction, alignment and integration.Gavage of veillonellayyyzzzyyy@sjtu.edu.cnA total of 8 mice stool samples (n=4 from DSS mice, n=4 from DSS mice with V. parvula colonization) were collected for untargeted metabolomics. MetabolomicsVeillonellauntargeted metabolitesinflammatory bowel diseaseVeillonellauntargeted metabolitesinflammatory bowel diseaseThe Orbitrap Exploris 120 mass spectrometer was used for its ability to acquire MS/MS spectra on information-dependent acquisition (IDA) mode in the control of the acquisition software (Xcalibur, Thermo). In this mode, the acquisition software continuously evaluates the full scan MS spectrum. The ESI source conditions were set as following: sheath gas flow rate as 50 Arb, Aux gas flow rate as 15 Arb, capillary temperature 320 °C, full MS resolution as 60000, MS/MS resolution as 15000, collision energy: SNCE 20/30/40, spray voltage as 3.8 kV (positive) or -3.4 kV (negative), respectively.falseUntargeted metabolomics of cecal contents from DSS induced colitis mice with and without Veillonella parvula colonizationCecal contents metabolomics analysis of DSS-induced colitis mice and DSS-induced colitis mice with V. parvula colonization.2025-08-122025-03-03MTBLS12276