MetaboLights

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were annotated in targeted mode from the predefined dMRM transitions (precursor and product ion pairs with optimized collision energies) and expected retention times of the facility's metabolite panel. Where isomers or isobars could not be resolved by the method (for example hexoses/myo-inositol, beta-alanine/sarcosine, SDMA/ADMA, 4-guanidinobutanoate/deoxycarnitine, guanidinosuccinate/N-acetylaspartate), all candidate identities are reported. The method does not separate D- and L-lactate, so lactate is reported as total lactate and mapped to the stereo-unspecified lactic acid entry (CHEBI:78320). ChEBI identifiers, formulae, SMILES and InChI were assigned by the submitters and checked against the ChEBI database; the mass_to_charge values in the metabolite assignment files are the theoretical precursor ions ([M+H]+, [M]+, [M+Na]+, [M-H]- or [M+CH3COO]-, as given in the modifications column) calculated from these structures, and the fragmentation column gives the dMRM transition (Q1 > Q3, as labelled in the mzML files). Retention times (minutes) were determined by the submitters from the mzML chromatograms: for each metabolite, the chromatographic peak whose area across the 39 study samples correlated best with the reported peak areas (Pearson r 0.85-1.00, median 0.997) was taken as the quantified peak, and its median apex time in the six pooled QC injections is reported. For 1-methylnicotinamide and acetylcholine the acquisition method uses a Q1 value 1 Da above the theoretical cation m/z.MetaboLightsPublicLiquid Chromatography MS - positive - hilicLiquid Chromatography MS - negative - hilicHydrophilic interaction liquid chromatography (HILIC) was performed on an Agilent 1290 Infinity II UHPLC system using two complementary methods. Positive ionization assay: ACQUITY UPLC BEH Amide column (1.7 µm, 100 mm x 2.1 mm i.d.; Waters); mobile phase A, 20 mM ammonium formate with 0.1% formic acid in water; mobile phase B, 0.1% formic acid in acetonitrile; gradient 0 min 95% B, 1.5 min 95% B, 17 min 45% B, 19 min 45% B, 20 min 95% B, 25 min 95% B; flow rate 400 µL/min; column temperature 25 °C; injection volume 2 µL. Negative ionization assay: iHILIC-(P) Classic column (5 µm, 100 mm x 2.1 mm, 200 Å, PEEK; HILICON AB); mobile phase A, 20 mM ammonium acetate and 20 mM ammonium hydroxide in water (pH 9.45); mobile phase B, 100% acetonitrile; gradient 0 min 90% B, 1.5 min 90% B, 8 min 50% B, 11 min 50% B, 12 min 45% B, 15 min 45% B, 16 min 90% B, 25 min 90% B; flow rate 300 µL/min; column temperature 30 °C; injection volume 2 µL.Baseline microbial ecology encodes probiotic responsiveness through distinct metabolic and network configurations.University of BernBahtiyar Yilmazmixturesolventfecesmass spectrometry assayFeces (1.5-12.7 mg) were extracted with 1000 µL of 80% methanol, sonicated in an ultrasonic bath and homogenized in lysis tubes with ceramic beads using a Precellys Cryolys tissue homogenizer. After centrifugation (21,000 g, 15 min, 4 °C), supernatants were evaporated to dryness and reconstituted in methanol, with the reconstitution volume normalized to the total protein content of each sample (BCA assay). Pooled QC samples representative of the entire sample set were analysed alongside the study samples: three conditioning injections of the pooled QC, a pooled QC dilution series (6.25, 12.5, 25, 50 and 100%) at the start and at the end of each batch, and a pooled QC after every 7-8 study samples (Pool001-Pool006). Solvent blanks were injected at the beginning (Blank001-Blank006) and end (BlankEnd001-BlankEnd003) of each batch, and a test mixture was injected at the start of each batch (Challmix in negative mode, Pretest in positive mode). Study samples were injected in randomized order.Mus musculusblankreference compoundhttps://www.ebi.ac.uk/metabolights/MTBLS15974Bahtiyar Yilmaz. University of Bern. bahtiyar.yilmaz@unibe.ch.Raw LC-MS/MS data were processed with Agilent MassHunter Quantitative Analysis software. Relative quantification was based on the extracted ion chromatogram (EIC) peak areas of the monitored MRM transitions. Signal intensity drift was corrected for each metabolite by fitting a locally weighted scatterplot smoothing (LOWESS) curve to the pooled QC samples analysed periodically throughout the batch, and metabolites with a coefficient of variation above 30% across the QC samples were removed. The metabolite assignment files report peak areas (ion counts) per sample as delivered by the metabolomics facility. The Agilent raw data were converted to mzML with ProteoWizard msConvert (version 3.0.24243) by the facility; the mzML files contain the dMRM chromatograms of all monitored transitions and are provided as derived data files. No data file was available for the final solvent blank of the negative-mode batch (BlankEnd003).Treatmentbahtiyar.yilmaz@unibe.chMale and female C57BL/6J mice (B6J-UniBe, 12-16 weeks of age) bred and maintained in flexible-film isolators at the Central Animal Facility of the University of Bern were randomly assigned to four groups: Control (drinking water only, n=8), DSS (n=11), Pre (n=10) and Post (n=10). Acute colitis was induced in the DSS, Pre and Post groups with 2% (w/v) dextran sulfate sodium (DSS) in the drinking water for 5 days, followed by 5 days of regular drinking water. The D-lactate-free probiotic cocktail Pro4-50 (Spectrum Ceuticals; Lactobacillus rhamnosus GG, Bifidobacterium lactis BL21, Bifidobacterium breve BB23 and Bifidobacterium longum BL25) was administered daily by oral gavage (10^9 CFU in 200 µL), either from the beginning of the experiment (Pre, preventive schedule) or from day 5 after the DSS period (Post, therapeutic schedule). Fecal samples were collected at the experimental endpoint (day 10). All mouse experiments were approved by the Commission for Animal Experimentation of Kanton Bern (licence BE121/2023).Metabolomicshydrophilic interaction chromatographyMetabolomicsMus musculuscolitisblanktargeted analysisstudy reference materialsolvent blankdextran sulfate sodiumtargeted metabolite profilingreference compound mixexperimental samplereference compoundmixtureliquid chromatography-tandem mass spectrometryAgilent 1290 Infinity II UHPLCsolventdilution series referencefecesAgilent 6495 Triple Quadrupolehydrophilic interaction chromatographyMetabolomicsMus musculuscolitisblanktargeted analysisstudy reference materialdextran sulfate sodiumsolvent blanktargeted metabolite profilingreference compound mixexperimental samplereference compoundmixtureliquid chromatography-tandem mass spectrometryAgilent 1290 Infinity II UHPLCsolventdilution series referencefecesAgilent 6495 Triple QuadrupoleAnalyses were performed on an Agilent 6495 triple quadrupole mass spectrometer with electrospray ionization, coupled to the 1290 UHPLC system and operated with MassHunter Acquisition software (Agilent Technologies). Data were acquired in dynamic multiple reaction monitoring (dMRM) mode with a total cycle time of 600 ms, using optimized collision energies for each metabolite of a targeted panel covering more than 400 polar and moderately polar metabolites of central carbon metabolism. Positive mode source parameters: drying gas temperature 230 °C, drying gas flow 14 L/min, nebulizer pressure 35 psi, sheath gas temperature 400 °C, sheath gas flow 12 L/min, nozzle voltage 500 V, capillary voltage +4000 V. Negative mode source parameters: drying gas temperature 290 °C, drying gas flow 14 L/min, nebulizer pressure 45 psi, sheath gas temperature 350 °C, sheath gas flow 12 L/min, nozzle voltage 0 V, capillary voltage -2000 V. The Scan m/z range given in each assay is the range of precursor ions of the reported metabolites.MANDELATESUBERATEQUINATE2-HYDROXYGLUTARIC ACID3-HYDROXYANTHRANILATECREATINECYTIDINEINOSINELACTATEDEOXYCYTIDINESUCCINATEGLUCURONATETHYMIDINE-MONOPHOSPHATEN-ACETYLPHENYLALANINEN-FORMYLMETHIONINEMALATEGLUCOSE 6-PHOSPHATESALICYLATEDEOXYURIDINE3,4 DIHYDROXYMANDELATE4-HYDROXY-3-METHOXYPHENYLGLYCOL3-HYDROXYBUTYRATEOXOADIPATE3-(2-HYDROXYPHENYL)PROPANOATEN-ACETYLGLUTAMATEMEVALONATEALLANTOINCYSTEATEFRUCTOSE 6-PHOSPHATEPYRUVATEASPARTATEHYDROXYPHENYLLACTATEPYRIDOXALN-ACETYLPROLINEURIDINEURACILDIHYDROURACILN-ACETYLLEUCINE4-HYDROXYBENZOATEXANTHINEGUANIDINOSUCCINATE or N-ACETYLASPARTATEURATEPYRIDOXINE3-DEHYDROSHIKIMATEUROCANATEHOMOGENTISATEFAD2,5-DIHYDROXYBENZOATEALPHA-KETOGLUTARATEDEOXYRIBOSEGLYCEROL 3-PHOSPHATEN-ACETYLNEURAMINATEGLYCERATEGLUCONATE2-HYDROXYBUTYRATEHYDROQUINONE3-HYDROXYPHENYLACETATETHREONINEN-ACETYLTRYPTOPHANfalseD-lactate-free probiotic treatment in colitisEffect of the D-lactate free bacteria in DSS-induced colitis mouse model2026-10-092026-10-09MTBLS15974MTBLC15725MTBLC18053MTBLC16020MTBLC16797MTBLC16303MTBLC35619MTBLC30831MTBLC27389MTBLC1582MTBLC29009MTBLC17645MTBLC16865MTBLC15728|MTBLC16244MTBLC18095MTBLC16974MTBLC17405MTBLC27823MTBLC18040MTBLC17780MTBLC16168MTBLC57589MTBLC15355MTBLC16335MTBLC17431MTBLC28498MTBLC16977MTBLC37023MTBLC18323MTBLC30754MTBLC16467MTBLC17196MTBLC16958|MTBLC15611MTBLC17750MTBLC15956MTBLC21949MTBLC18127MTBLC16347MTBLC15727MTBLC15354MTBLC16349MTBLC16737MTBLC16283MTBLC28717MTBLC17256MTBLC17172MTBLC23673MTBLC25682|MTBLC17929MTBLC17724MTBLC28918MTBLC16000MTBLC16015MTBLC18050MTBLC82952MTBLC15428MTBLC17687MTBLC16344MTBLC16235MTBLC16750MTBLC84834MTBLC18295MTBLC15971MTBLC16255MTBLC17368MTBLC17191MTBLC70819MTBLC18344MTBLC77086MTBLC15603MTBLC18019MTBLC4208|MTBLC4093|MTBLC37721|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|MTBLC21547MTBLC44747MTBLC17594MTBLC17385MTBLC17596MTBLC78320MTBLC30797MTBLC35825MTBLC17710MTBLC17533MTBLC17786MTBLC17012MTBLC16259MTBLC21560MTBLC74640MTBLC16552MTBLC15753MTBLC17310MTBLC16709MTBLC32816MTBLC17521MTBLC16914MTBLC9300MTBLC15741MTBLC16857MTBLC17013MTBLC17568MTBLC17775MTBLC16704MTBLC30817MTBLC17712CHEBI:15725CHEBI:18053CHEBI:16020CHEBI:16797CHEBI:16303CHEBI:35619CHEBI:30831CHEBI:27389CHEBI:1582CHEBI:29009CHEBI:17645CHEBI:16865CHEBI:15728|CHEBI:16244CHEBI:18095CHEBI:16974CHEBI:17405CHEBI:27823CHEBI:18040CHEBI:17780CHEBI:16168CHEBI:57589CHEBI:15355CHEBI:16335CHEBI:17431CHEBI:28498CHEBI:16977CHEBI:37023CHEBI:18323CHEBI:30754CHEBI:16467CHEBI:17196CHEBI:16958|CHEBI:15611CHEBI:17750CHEBI:15956CHEBI:21949CHEBI:18127CHEBI:16347CHEBI:15727CHEBI:15354CHEBI:16349CHEBI:16737CHEBI:16283CHEBI:28717CHEBI:17256CHEBI:17172CHEBI:23673CHEBI:25682|CHEBI:17929CHEBI:17724CHEBI:28918CHEBI:16000CHEBI:16015CHEBI:18050CHEBI:82952CHEBI:15428CHEBI:17687CHEBI:16344CHEBI:16235CHEBI:16750CHEBI:84834CHEBI:18295CHEBI:15971CHEBI:16255CHEBI:17368CHEBI:17191CHEBI:70819CHEBI:18344CHEBI:77086CHEBI:15603CHEBI:18019CHEBI:4208|CHEBI:4093|CHEBI:37721|CHEBI:17268CHEBI:16643CHEBI:16628CHEBI:17509CHEBI:84634CHEBI:17311CHEBI:40992CHEBI:139582CHEBI:63153CHEBI:17768CHEBI:15846CHEBI:35704CHEBI:17154CHEBI:15940CHEBI:16440CHEBI:18102CHEBI:17490CHEBI:46905CHEBI:25858CHEBI:18397CHEBI:17295CHEBI:17964CHEBI:17203CHEBI:53210CHEBI:17258CHEBI:17148CHEBI:17015CHEBI:15414CHEBI:17115CHEBI:28790CHEBI:84644CHEBI:15891CHEBI:18385CHEBI:17748CHEBI:17821CHEBI:18123CHEBI:18139CHEBI:16765CHEBI:16828CHEBI:15760CHEBI:17895CHEBI:18261CHEBI:16414CHEBI:18107CHEBI:17189CHEBI:1148CHEBI:17084CHEBI:16104CHEBI:27637CHEBI:30918CHEBI:15793CHEBI:20067CHEBI:17445CHEBI:1576CHEBI:30763CHEBI:15676CHEBI:30915CHEBI:17053CHEBI:16919CHEBI:17285CHEBI:17562CHEBI:15698CHEBI:28816CHEBI:16450CHEBI:15901CHEBI:16238CHEBI:15946CHEBI:33198CHEBI:4170CHEBI:47952CHEBI:33508CHEBI:15978CHEBI:17072|CHEBI:21547CHEBI:44747CHEBI:17594CHEBI:17385CHEBI:17596CHEBI:78320CHEBI:30797CHEBI:35825CHEBI:17710CHEBI:17533CHEBI:17786CHEBI:17012CHEBI:16259CHEBI:21560CHEBI:74640CHEBI:16552CHEBI:15753CHEBI:17310CHEBI:16709CHEBI:32816CHEBI:17521CHEBI:16914CHEBI:9300CHEBI:15741CHEBI:16857CHEBI:17013CHEBI:17568CHEBI:17775CHEBI:16704CHEBI:30817CHEBI:17712