Compounds were identified by comparison to library entries of purified standards or recurrent unknown entities. Metabolon maintains a library based on authenticated standards that contains the retention time/index (RI), mass to charge ratio (m/z), and chromatographic data (including MS/MS spectral data) on all molecules present in the library. More than 4500 commercially available purified standard compounds have been acquired and registered into LIMS for analysis on all platforms for determination of their analytical characteristics. Additional mass spectral entries have been created for structurally unnamed biochemicals, which have been identified by virtue of their recurrent nature (both chromatographic and mass spectral). These compounds have the potential to be identified by future acquisition of a matching purified standard or by classical structural analysis.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase","Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["All methods utilize a Waters ACQUITY ultra-performance liquid chromatography (UPLC). Each reconstitution solvent contains a series of standards at fixed concentrations to ensure injection and chromatographic consistency. Method 1/Pos 1: One aliquot is analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract is gradient-eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 um) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Method 2/Pos 2: A second aliquot is also analyzed using acidic positive ion conditions, but is chromatographically optimized for more hydrophobic compounds. In this method, the extract is gradient eluted from the aforementioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA, and is operated at an overall higher organic content. Method 3/Neg 1: A third aliquot is analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts are gradient-eluted from the column using methanol and water, however with 6.5 mM Ammonium Bicarbonate at pH 8. Method 4/Neg 2: The fourth aliquot is analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 um) using a gradient consisting of water and acetonitrile with 10 mM Ammonium Formate, pH 10.8.
"],"publication":["Butyrate epigenetically licenses sustained epithelial-T cell crosstalk for intestinal immune tolerance. 10.1038/s41467-026-75600-w. PMID:42457691"],"submitter_affiliation":["Northwestern University"],"submitter_name":["Tianming Yu"],"organism_part":["intestinal epithelial cell"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Samples are prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards are added prior to the first step in the extraction process for QC purposes. Samples are extracted with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) to precipitate protein and dissociate small molecules bound to protein or trapped in the precipitated protein matrix, followed by centrifugation to recover chemically diverse metabolites. The resulting extract is divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods using positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS using negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS using negative ion mode ESI, and one reserved for backup. Samples are placed briefly on a TurboVap® (Zymark) to remove the organic solvent and stored overnight under nitrogen. In preparation for analysis, samples are then reconstituted in solvents compatible to each of the four methods.
"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14301"],"author":["Yu Tianming. tianming.yu@northwestern.edu.","Cong Yingzi. Northwestern University Feinberg School of Medicine. yingzi.cong@northwestern.edu."],"data_transformation_protocol":["Raw data were extracted, peak-identified, and QC processed using Metabolon's hardware and software. These systems are built on a web-service platform utilizing Microsoft's .NET technologies, which run on high-performance application servers and fiber-channel storage arrays in clusters to provide active failover and load-balancing.
"],"study_factor":["Biospecimen","Treatment"],"submitter_email":["tianming.yu@northwestern.edu"],"sample_collection_protocol":["Immortalized Mouse Small Intestinal Epithelial (MSIE) cells were cultured in 1640 RPMI media supplemented with Penicillin/Streptomycin , Insulin-Transferrin-Selenium, and 5% Fetal bovine serum in the presence or absence of sodium butyrate (2 mM) for 2 days. Supernatants were filtered using Amicon 3K centrifugal filters, and the <3 kDa fraction was collected for untargeted metabolomics analysis. In parallel, cell pellets were harvested for untargeted metabolomics. Untargeted metabolic profiling was performed by liquid chromatography (LC)/tandem mass spectrometry (MS) using Metabolon Inc. platform (Durham, NC, US).
"],"omics_type":["Metabolomics"],"study_design":["ultra-performance liquid chromatography-mass spectrometry","Mus musculus","Intestinal homeostasis","intestinal epithelial cell","untargeted analysis","Waters ACQUITY UPLC system","Intestinal Epithelial cells metabolites","Q Exactive Plus","tandem mass spectrometer","Metabolon (United States)","untargeted metabolite profiling","experimental sample"],"curator_keywords":["ultra-performance liquid chromatography-mass spectrometry","Mus musculus","Intestinal homeostasis","intestinal epithelial cell","untargeted analysis","Waters ACQUITY UPLC system","Intestinal Epithelial cells metabolites","Q Exactive Plus","tandem mass spectrometer","Metabolon (United States)","untargeted metabolite profiling","experimental sample"],"mass_spectrometry_protocol":["A Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution was used. The MS analysis alternates between MS and data-dependent MSn scans using dynamic exclusion.
"],"metabolite_name":["pyridoxate","inosine","2'-deoxyadenosine 5'-monophosphate","4-hydroxyphenylpyruvate","N-acetylthreonine","sedoheptulose-7-phosphate","1-palmitoyl-GPI (16:0)","N-acetylisoleucine","1-docosahexaenoyl-GPE (22:6)*","2-hydroxystearate","hippurate","hypoxanthine","thymidine","N-palmitoylglycine","6-keto prostaglandin F1alpha","N6-carbamoylthreonyladenosine","glycocholate","2-hydroxynervonate*","coenzyme A","N-formylphenylalanine","1-oleoyl-GPI (18:1)","benzoate","2-stearoyl-GPE (18:0)*","glycochenodeoxycholate","sulfate*","thiamin monophosphate","pyridoxal phosphate","tauroursodeoxycholate","5-oxoproline","UDP-glucuronate","thymidine 3'-monophosphate","1-linoleoyl-GPI (18:2)*","2'-deoxyguanosine","N-lactoyl phenylalanine","pantothenate","kynurenate","2-hydroxypalmitate","citrate","indolelactate","penicillin G","nicotinamide adenine dinucleotide (NAD+)","pyridoxine (vitamin B6)","taurocholate","thymidine 5'-monophosphate","5,6-dihydrouridine","N6-succinyladenosine","taurochenodeoxycholate","glycodeoxycholate","N-acetyltaurine","guanosine","2-palmitoleoyl-GPC (16:1)*","N-formylmethionine","3-phosphoglycerate","inositol trisphosphate","xanthosine","phenol sulfate","linoleoyl ethanolamide","palmitate (16:0)","histidine","2-hydroxybehenate","N-acetylalanine","tyrosylglycine","phenylacetylglycine","N-lactoyl tyrosine","3-methyl-2-oxovalerate","2'-deoxyadenosine 3'-monophosphate","CoA-glutathione*","cholate","4-acetamidobenzoate","taurodeoxycholate","N-lactoyl valine","taurine","N-acetylphenylalanine","3'-dephosphocoenzyme A","glycerol","N-acetylvaline","xanthurenate","phenol red","pantoate","malate","N-acetylmethionine","4-methyl-2-oxopentanoate","2'-deoxyinosine","tauro-beta-muricholate","2'-O-methyluridine","2'-deoxyuridine","riboflavin (vitamin B2)","uridine","phosphopantetheine","genistein","erythrose","N-delta-acetylornithine","N6-acetyllysine","p-cresol sulfate","S-(1,2-dicarboxyethyl)glutathione","pseudouridine","12,13-DiHOME","daidzein","N-formylkynurenine","3-(4-hydroxyphenyl)lactate","N-acetylleucine","1-arachidonoyl-GPI (20:4)*","nicotinate","HEPES","9,10-DiHOME","O-sulfo-tyrosine","stearidonate (18:4n3)","docosadienoate (22:2n6)","2-hydroxydecanoate","thymine"],"pubmed_abstract":["Intestinal epithelial cells (IEC) are the primary cell type in direct contact with stimuli from the luminal microbiota, playing a critical role in host-microbe interactions. However, how IECs communicate with underlying immune cells to maintain homeostasis remains poorly understood. In addition, the mechanisms by which IECs sense microbiota-derived stimuli to initiate this crosstalk are not yet fully understood. Here, we demonstrate that oral administration of the gut microbiota metabolite butyrate induces sustained IL-10 production in CD4⁺ T cells, conferring long-lasting protection against intestinal inflammation even after treatment withdrawal. This persistent immunoregulatory effect is also observed in germ-free mice, indicating the establishment of a butyrate-conditioned intestinal environment. By metabolomic profiling, we identify N1-acetylspermidine as a metabolite contributing to the IL-10-inducing activity of butyrate-treated IEC-conditioned medium. Mechanistically, butyrate induces sustained transcriptional and epigenetic activation of the acetylpolyamine biosynthetic enzyme Sat1 in IECs, which catalyzes the acetylation of spermidine to generate N1-acetylspermidine, and this activation persists after butyrate withdrawal. Together, our findings reveal a mechanism by which butyrate sensing establishes persistent crosstalk between IECs and T cells, thereby maintaining intestinal immune tolerance through epigenetic regulation and reprogramming of epithelial metabolism."],"pubmed_title":["Butyrate epigenetically licenses sustained epithelial-T cell crosstalk for intestinal immune tolerance."],"pubmed_authors":["Yu Tianming T, Yang Wenjing W, Bilotta Anthony J AJ, Yao Suxia S, Lee Jeong-Heon JH, Zhao Qihong Q, Zhou Jia J, Ordog Tamas T, Dulai Parambir S PS, Cong Yingzi Y"],"additional_accession":[]},"is_claimable":false,"name":"Butyrate epigenetically licenses sustained epithelial-T cell crosstalk for intestinal immune tolerance","description":"Butyrate, one of the most abundant microbial-derived metabolites in the gut, is important in regulating intestinal homeostasis. In this study, we used untargeted global metabolomics to landscape the intestinal epithelial cellular metabolites changed by butyrate treatment.
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