Direct injection of analytical standards were used in calibration curves.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - alternating - reverse-phase","Liquid Chromatography MS -negative - reverse-phase"],"chromatography_protocol":["SCFA: The supernatants were then transferred to brown glass vials for immediate UPLC-MS/MS analysis. The UPLC-MS/MS system consisted of an Agilent 1290 Infinity II UPLC coupled to a ThermoFisher TSQ Quantiva triple quadrupole mass spectrometer. Chromatographic separation was performed using a Waters ACQUITY BEH C18 column (1.7 μm, 2.1 × 100 mm) maintained at 40°C with a 5 μL injection volume. The mobile phase comprised water with 0.1% formic acid (Phase A) and acetonitrile with 0.1% formic acid (Phase B) at a flow rate of 0.3 mL/min. An optimized gradient was implemented as follows: 5% B for 5 minutes, 5-55% B over 12 minutes, 100% B for 1 minute, followed by 2 minutes at 5% B.
Tryptophan: The analysis was performed using an Agilent 1290 ultra-high performance liquid chromatograph (UHPLC) system coupled to a Thermo Quantiva triple quadrupole mass spectrometer operating in multiple reaction monitoring (MRM) mode. Chromatographic separation was achieved using a Waters XSelect Premier HSS T3 column (2.5 μm, 2.1 × 150 mm) with a 10-minute gradient at around 400 bar, a flow rate of 0.4 mL/min, and an injection volume of 5 µL. The gradient program was as follows: starting at 97% A/3% B and maintaining these conditions for 0.45 minutes, transitioning to 70% A/30% B at 1.2 minutes, then to 40% A/60% B by 2.7 minutes (held until 3.75 minutes), followed by a transition to 5% A/95% B at 4.5 minutes (maintained until 6.6 minutes), and finally returning to the initial conditions at 6.75 minutes with re-equilibration until 10 minutes.
"],"publication":["Functional microbiome shifts are associated with neuroinflammatory outcomes under dietary interventions in multiple sclerosis."],"submitter_name":["Friederike Gutmann"],"submitter_affiliation":["Charité - Universitätsmedizin Berlin"],"organism_part":["blood serum","feces"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["SCFAs: The final derivatization parameters, taken from Han et al. (https://doi.org/10.1016/j.aca.2014.11.015), were implemented in our lab and used to analyze pure standards dissolved in 50% (v/v) ACN:H2O, and to evaluate the distribution of SCFA and KB in commercial mouse plasma. Briefly, 40 μL of matrix, either mouse plasma or mixed standard solution, was mixed in glass vials with 20 μL of 200 mM 3NPH, 20 μL of 120 mM EDC with 6% pyridine, and 10 μL of 50 μM ISTDs, and incubated at 40°C for 30 min. Standard solutions were prepared fresh and kept at room temperature for the short time until derivatization. After incubation, 410 μL of 10% (v/v) ACN:H2O was added, and the samples were centrifuged at 5500×g for 20 min at 20°C. The supernatants were transferred to brown glass vials and directly subjected to UPLC-MS/MS analysis. Commercial mouse plasma was thawed and kept on ice until derivatization using the same method as above.
Tryptophan: In this study, 152 serum and 143 fecal samples underwent analysis over 3 batches. Concurrent quantification of 34 tryptophan metabolites and 9 branched-chain amino acids in two separate assays was conducted using a methanol extraction method with a 90% concentration. The mobile phase system consisted of two components: Phase A, comprising 0.2% formic acid in water, and Phase B, consisting of 0.2% formic acid in methanol. Fecal samples were prepared by dissolving them in water to achieve a concentration of 50 mgStool/mL. For the extraction process, 50 μL of the biological sample was combined with 100 μL of a chilled solution containing 90% methanol, 0.2% formic acid, and 0.02% ascorbic acid, along with internal standards as described elsewhere. The extraction protocol involved vortexing the samples for 30 seconds, followed by centrifugation at 1,000 rpm for 10 minutes at 4°C, and incubation at -20°C for 1 hour. Subsequently, the samples were centrifuged again at 12,000 rpm for 10 minutes at 4°C.
"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15689"],"author":["Friederike Gutmann. Charité - Universitätsmedizin Berlin. friederike.gutmann@mdc-berlin.de.","Jennifer Kirwan. Veterinary Metabolomics, University of Veterinary Medicine Vienna. Jennifer.Kirwan@vetmeduni.ac.at."],"data_transformation_protocol":["Data processing per matrix and method utilized Skyline software (v. 22.2.0.527) for peak integration and quantification, as well as R (v. 4.2.3). Peaks were normalized to corresponding internal standards. Metabolite areas were retained if they were quantifiable or fell between the limit of detection and the lower limit of quantification in at least 60% of samples across all statistical groups. A signal-to-noise filter was applied, requiring signals to exceed at least 3-fold the corresponding peak area observed in the blank sample. Batch correction was performed using pooled QC sample-based robust locally estimated scatterplot smoothing signal correction from the statTarget package (v. 1.28.0) with a smoothing parameter set to 0.75. Missing stool tryptophan values (n = 13) were imputed using half minimum value imputation. Compound retention required that the relative standard deviation (RSD) of QCs did not exceed 60% in stool and 30% in serum. QC samples reflect technical variability alone, whereas variation among biological samples captures both technical and true biological differences. To ensure that retained metabolites exhibited biologically meaningful variation rather than analytical noise, only metabolites with a per batch biological sample RSD within samples that was at least 20 % larger than the per batch RSD measured in QCs for that batch in all batches were included in the downstream analysis. Processed and corrected peak areas are referred to as AUC throughout the manuscript.
"],"study_factor":["DietGroup","Visit"],"submitter_email":["fgutmann@gmx.de"],"sample_collection_protocol":["The original block randomization of participants was done by an external statistician and included stratification according to DMT use, gender, and T2 lesion load. Cerebral MRI scans were acquired at baseline and at 9 months using standardized 3D T1-weighted MPRAGE and 3D FLAIR sequences, with images co-registered to baseline in MNI space. T2-hyperintense lesions were manually segmented by two blinded, experienced raters. T2 lesion count and total lesion volumes were extracted from binary masks using FSL tools. Participants could be discontinued from the study if they withdrew consent, met an exclusion criterion, did not comply with the study protocol, or had a medical reason to stop the intervention. Compliance was defined, for all three groups, as attending at least 8 of the 10 group sessions and all 6 study visits. Food records were used to check compliance with the assigned intervention. Intervention adherence was followed longitudinally through group-session and study-visit attendance, food records, and intervention-specific monitoring. KD participants measured blood ketone levels at home using a portable ketone monitoring device (GlucoMen LX plus) and discussed the results with the study team during scheduled appointments. In the KD group, most blood ketone measurements had to be at least 0.5 mmol/L. In the FD group, participants attended additional meetings during each of the three fasting periods, which allowed the physician and counselor to assess their compliance. Blood serum in plain tubes and whole stool samples from 76 per-protocol patients were acquired from the NAMS study and stored at -80°C. Additionally, 29 baseline stool samples from dropout patients were acquired. Stool samples were homogenized using an in-house-produced device.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific TSQ Quantiva","Metabolomics","Skyline","targeted analysis","multiple sclerosis","Tryptophan","Homo sapiens","experimental sample","data-independent acquisition","Agilent 1290 Infinity UHPLC","blood serum","Agilent 1290 Infinity II UHPLC","Serum","Max Delbrück Center","Short Chain Fatty Acid","feces","Berlin Institute of Health at Charité - Universitätsmedizin Berlin"],"curator_keywords":["Thermo Scientific TSQ Quantiva","Metabolomics","Skyline","targeted analysis","multiple sclerosis","Tryptophan","Homo sapiens","experimental sample","data-independent acquisition","Agilent 1290 Infinity UHPLC","blood serum","Agilent 1290 Infinity II UHPLC","Serum","Max Delbrück Center","Short Chain Fatty Acid","feces","Berlin Institute of Health at Charité - Universitätsmedizin Berlin"],"mass_spectrometry_protocol":["SCFA: Analysis were done using a ThermoFisher TSQ Quantiva triple quadrupole mass spectrometer. Multiple reaction monitoring (MRM) was performed in negative electrospray ionization mode with a spray voltage of 2500 V, an ion transfer tube temperature of 342°C, and a vaporizer temperature of 300°C. Quality control samples, as described previously, were also employed in this analysis.
Tryptophan: A ThermoFisher TSQ Quantiva triple quadrupole mass spectrometer operating in multiple reaction monitoring (MRM) mode was used for analysis. A calibration curve consisting of a mix of 34 tryptophan standards plus TMA and TMAO was run at 11 concentrations in the matrix background of charcoal-stripped plasma. Level 6 of this mix and a solvent blank were run every 6 samples as an extra quality check. Pooled quality control samples (QCs) were prepared by pooling all of the samples and run at the beginning, end, and every 6 samples during each batch. 6 extracted charcoal-stripped plasma samples were run before 6 extracted water samples at the end of the sequence.
"],"metabolite_name":["isovaleric acid","2-methylbutyric acid","butyric acid","3-hydroxy-3-methylbutyric acid","isobutyric acid","propanoic acid","acetic acid","3-hydroxybutyric acid","hexanoic acid","acetoacetic acid","valeric acid"],"additional_accession":[]},"is_claimable":false,"name":"Nutritional Approaches in Multiple Sclerosis","description":"The aim of this project is to characterize the influence of a ketogenic diet and intermittent therapeutical fasting on the course of the disease, as measured by T2-hyperintense cerebral lesions with magnetic resonance tomography (MRT) in patients with multiple sclerosis (RRMS). The investigators expect in both intervention groups fewer cerebral T2 lesions occurring after 18 months in comparison to the control group and as detectable by MRT. According to current recommendations of the German Society of Nutrition (DGE), the control group receives a vegetarian-focused, anti-inflammatory diet.","dates":{"publication":"2026-09-23","submission":"2026-09-16"},"accession":"MTBLS15689","cross_references":{"MetaboLights":["MTBLC18112","MTBLC30896","MTBLC27830","MTBLC16827","MTBLC16031","MTBLC28911","MTBLC19297","MTBLC18388","MTBLC27823","MTBLC18484","MTBLC18390","MTBLC15643","MTBLC28177","MTBLC16882","MTBLC17308","MTBLC16826","MTBLC35581","MTBLC16800","MTBLC16801","MTBLC17890","MTBLC16022","MTBLC16828","MTBLC16825","MTBLC16469","MTBLC16865","MTBLC16796","MTBLC28082","MTBLC15980","MTBLC17325","MTBLC28790","MTBLC27824","MTBLC16489","MTBLC18139","MTBLC15724","MTBLC15366","MTBLC20067","MTBLC50540","MTBLC30768","MTBLC30772","MTBLC16135","MTBLC30813","MTBLC28484","MTBLC30814","MTBLC30776","MTBLC15344"],"ChEBI":["CHEBI:18112","CHEBI:30896","CHEBI:27830","CHEBI:16827","CHEBI:16031","CHEBI:28911","CHEBI:19297","CHEBI:18388","CHEBI:27823","CHEBI:18484","CHEBI:18390","CHEBI:15643","CHEBI:28177","CHEBI:16882","CHEBI:17308","CHEBI:16826","CHEBI:35581","CHEBI:16800","CHEBI:16801","CHEBI:17890","CHEBI:16022","CHEBI:16828","CHEBI:16825","CHEBI:16469","CHEBI:16865","CHEBI:16796","CHEBI:28082","CHEBI:15980","CHEBI:17325","CHEBI:28790","CHEBI:27824","CHEBI:16489","CHEBI:18139","CHEBI:15724","CHEBI:15366","CHEBI:20067","CHEBI:50540","CHEBI:30768","CHEBI:30772","CHEBI:16135","CHEBI:30813","CHEBI:28484","CHEBI:30814","CHEBI:30776","CHEBI:15344"]}}