MetaboLights

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fatty acids were identified by retention time and quantifier/qualifier ions matched to authentic standards (calibration series) analysed in the same batch. Isovaleric and 2-methylbutyric acid co-elute and were quantified on distinct fragment ions (m/z 60 and 74). The other acids of the panel (2-methylhexanoic, 2-propylvaleric, 3-methylvaleric, 4-methylhexanoic, 4-methylvaleric, crotonic, heptanoic and hexanoic acid) were not detected and are not reported. ChEBI identifiers, formulae, SMILES and InChI were assigned by the submitters and checked against the ChEBI database; mass_to_charge values in the metabolite assignment file are the SIM quantifier ions and retention times are given in minutes.MetaboLightsPublicGas Chromatography MS - positive - high-polarityGas chromatography was performed on a Thermo Scientific TRACE 1610 gas chromatograph with a DB-FFAP column (30 m x 0.25 mm i.d. x 0.25 µm film; Agilent Technologies); helium carrier gas at a constant flow of 1.2 mL/min; oven 40 °C, then 10 °C/min to 200 °C and 40 °C/min to 240 °C, held for 3 min; splitless injection of 1.0 µL at 240 °C.Baseline microbial ecology encodes probiotic responsiveness through distinct metabolic and network configurations.Bahtiyar YilmazUniversity of Bernmixturesolventfecesmass spectrometry assayFeces (10 mg) were homogenized in 1000 µL of water with 9-12 ceramic beads using a Precellys Cryolys homogenizer below 10 °C and centrifuged (15 min, 15,000 rpm, 4 °C). A 100 µL aliquot of the supernatant was extracted by sequential addition of 10 µL of 15% phosphoric acid, 10 µL of internal standard solution (13C- or deuterium-labelled acetic, propionic, butyric, isovaleric, valeric, 4-methylvaleric, hexanoic, heptanoic and valproic acid) and 140 µL of methyl tert-butyl ether (MTBE), vortexed for 10 s, shaken for 10 min at room temperature and centrifuged (15 min, 15,000 rpm, 4 °C); 100 µL of the upper organic phase was transferred to an insert vial (method of Lotti et al. 2017, doi:10.1007/s00216-017-0493-5). The batch included solvent blanks (Blank1-Blank9), an extraction blank (B-Extracted), 13 calibration standards (Cal0-Cal12; 0.1-500 µM, acetic acid 0.2-1000 µM, in water with internal standard), QC standards at low, mid and high concentration, and four pooled fecal QC samples interspersed among the randomized study samples.Mus musculusblankreference compoundhttps://www.ebi.ac.uk/metabolights/MTBLS15952Bahtiyar Yilmaz. University of Bern. bahtiyar.yilmaz@unibe.ch.SIM data were processed with TraceFinder Clinical 4.1 (Thermo Fisher Scientific). Concentrations were calculated from analyte-to-internal-standard peak area ratios using 13-level calibration curves (Cal0-Cal12), with automatic peak integration and manual review. Fecal concentrations (µmol/g fresh weight) reported in the metabolite assignment file were calculated as extract concentration (µM) x extraction volume (1 mL) / fecal mass (10 mg); values below the limit of quantification are left empty. Concentrations are reported for the study samples and the pooled fecal QC samples only. Coefficients of variation in the pooled QC samples were 0.5-13% for the six reported acids.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 three groups: DSS (n=7), Pre (n=10) and Post (n=9). Acute colitis was induced 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); DSS mice received no probiotic. 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). This cohort is independent of the cohort analysed in the companion LC-MS/MS polar metabolomics study.MetabolomicsMetabolomicsMus musculusblankcolitisgas chromatography-mass spectrometrytargeted analysisstudy reference materialsolvent blankquality control materialdextran sulfate sodiumThermo Scientific TSQ 9610targeted metabolite profilingsample preparation blankreference compound mixexperimental samplereference compoundmixturesolventfecesThermo Scientific TRACE 1610 GCMetabolomicsMus musculusblankcolitisgas chromatography-mass spectrometrytargeted analysisstudy reference materialsolvent blankquality control materialdextran sulfate sodiumThermo Scientific TSQ 9610targeted metabolite profilingsample preparation blankreference compound mixexperimental samplereference compoundmixturesolventfecesThermo Scientific TRACE 1610 GCA Thermo Scientific TSQ 9610 triple quadrupole mass spectrometer was operated in electron ionization mode at 70 eV using selected ion monitoring (SIM) with a dwell time of 2 ms per ion and a scan range of m/z 40-160; the quantifier and qualifier ions of each acid are listed in the metabolite assignment file.Valeric acid2-methylbutyric acidPropionic acidIsovaleric acidAcetic acidButyric acidfalseFecal short-chain fatty acids in DSS-induced colitis mice treated with a D-lactate-free probioticTargeted GC-MS quantification of short- and branched-chain fatty acids in feces of C57BL/6J (B6J-UniBe) mice with acute dextran sulfate sodium (DSS)-induced colitis. Mice received the D-lactate-free probiotic consortium Pro4-50 by daily oral gavage either from the start of the experiment (Pre, n=10) or after the 5-day DSS period (Post, n=9), or no probiotic (DSS, n=7). Feces collected at day 10 were extracted with MTBE and analysed on a TRACE 1610 GC coupled to a TSQ 9610 triple quadrupole mass spectrometer in SIM mode using stable isotope-labelled internal standards and 13-level calibration curves. Acetate, propionate, butyrate, isovalerate, 2-methylbutyrate and valerate are reported in µmol/g feces. This dataset accompanies a companion MetaboLights study of targeted polar fecal metabolomics (LC-MS/MS) in an independent cohort of the same experimental model.2026-10-082026-10-08MTBLS15952MTBLC15366MTBLC30768MTBLC30772MTBLC28484MTBLC37070MTBLC17418CHEBI:15366CHEBI:30768CHEBI:30772CHEBI:28484CHEBI:37070CHEBI:17418