Metabolite identification was performed by matching the accurate precursor m/z values (mass tolerance < 10 ppm), retention times (RT), and MS/MS fragmentation spectra against an in-house database (BiotreeDB V3.0) established with authentic chemical standards. Isotopic peaks and adduct ions were annotated using the CAMERA R package. To ensure annotation reliability, all identified metabolites were assigned to confidence Level 2 or higher according to the Metabolomics Standards Initiative (MSI) criteria, and all results were manually curated and cross-validated by experienced analysts to remove false positive identifications. The final identification results were compiled into a comprehensive data matrix containing metabolite names, HMDB IDs, KEGG IDs, retention times, m/z values, adduct information, and peak intensities for subsequent statistical and functional analyses.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Chromatographic separation was performed on a Vanquish UHPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Exploris 120 mass spectrometer. Samples were separated on a Waters ACQUITY UPLC BEH Amide column (2.1 mm × 50 mm, 1.7 μm) with HILIC mode. The column temperature was maintained at 25 °C, and the autosampler was kept at 4 °C. The mobile phase consisted of (A) water containing 25 mM ammonium acetate and 25 mM ammonium hydroxide (pH 9.75) and (B) acetonitrile. The flow rate was 0.3 mL/min, and the injection volume was 2 μL. The gradient elution program was as follows: 0–1.5 min, 98% B; 1.5–12 min, B linearly decreased from 98% to 2%; 12–14 min, 2% B maintained; 14–14.1 min, B increased from 2% to 98%; 14.1–17 min, 98% B maintained for re-equilibration.
"],"publication":["Untargeted metabolomics analysis of intestinal contents in Common Carp."],"submitter_affiliation":["Henan normal university"],"submitter_name":["Peng Pang"],"organism_part":["Intestinal Content"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Samples (intestinal contents) were slowly thawed at 4 C. An appropriate aliquot was mixed with pre-cold methanol/acetonitrile/water (2:2:1, v/v/v) containing deuterated internal standards, vortexed, and ultrasonicated at low temperature for 30 min, then incubated at -20 C for 10 min. After centrifugation at 14,000 x g for 20 min at 4 C, the supernatant was collected and vacuum-dried. The residue was reconstituted in 100 uL of acetonitrile/water (1:1, v/v), vortexed, and centrifuged again at 14,000 x g for 15 min at 4 C. The final supernatant was used for LC-MS/MS analysis. A pooled quality control (QC) sample was prepared by combining equal volumes of all individual sample supernatants, and was injected regularly throughout the analytical run to monitor system stability and data reproducibility.
"],"organism":["Cyprinus carpio"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15296"],"author":["Peng Pang. Henan normal university. pangp1998@163.com."],"data_transformation_protocol":["Raw MS data files (.raw) were converted to mzXML format using ProteoWizard (MSConvert) software. The converted data were then processed using XCMS software for peak detection, retention time alignment, and peak area extraction. The following parameters were applied for peak picking: centWave m/z = 10 ppm, peakwidth = c(10, 60), and prefilter = c(10, 100). For peak grouping, bandwidth (bw) = 5, mzwid = 0.025, and minfrac = 0.5 were used. Isotope and adduct annotations were performed using the CAMERA (Collection of Algorithms of Metabolite Profile Annotation) R package. Variables with more than 50% nonzero measurement values in at least one group were retained for further analysis. Metabolite identification was achieved by matching the accurate m/z values (< 10 ppm) and MS/MS fragmentation spectra against an in-house database (BiotreeDB V3.0) established with authentic standards. The resulting data matrix containing metabolite identities, retention times, and peak intensities was then subjected to subsequent statistical analyses.
"],"study_factor":["Probiotics"],"submitter_email":["pangp1998@163.com"],"sample_collection_protocol":["Intestinal contents were collected from common carp after a 56-day dietary intervention. Fish were fasted for 24 h, anesthetized with MS-222, and dissected under sterile conditions. The gut contents were immediately frozen in liquid nitrogen and stored at -80 C prior to LC-MS/MS analysis.
"],"omics_type":["Metabolomics"],"study_design":["Gut microbiota","Metabolomics","Probiotics","Glycolipid metabolism","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","common carp","Intestinal Content","Cyprinus carpio","Agilent 1290 Infinity LC","experimental sample"],"curator_keywords":["Gut microbiota","Metabolomics","Probiotics","Glycolipid metabolism","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","common carp","Cyprinus carpio","Intestinal Content","Agilent 1290 Infinity LC","experimental sample"],"mass_spectrometry_protocol":["Mass spectrometry analysis was performed on an Orbitrap Exploris 120 mass spectrometer (Thermo Fisher Scientific) equipped with an electrospray ionization (ESI) source operating in both positive and negative ion modes. Full MS scans were acquired over the m/z range of 80–1200 Da at a resolution of 60,000 (FWHM) with an accumulation time of 100 ms. Data-dependent acquisition (DDA) was employed for MS/MS fragmentation, with MS/MS scans acquired over the m/z range of 70–1200 Da at a resolution of 15,000, accumulation time of 50 ms, and stepped normalized collision energy (NCE) of 20/30/40. The ion source parameters were set as follows: ion source gas 1 (sheath gas) at 60 arbitrary units, ion source gas 2 (auxiliary gas) at 60 arbitrary units, curtain gas at 30 arbitrary units, source temperature at 600 °C, and spray voltage at +3.8 kV (positive) and −3.4 kV (negative). The dynamic exclusion time was set to 4 s to avoid redundant fragmentation of abundant precursor ions.
"],"additional_accession":[]},"is_claimable":false,"name":"Untargeted metabolomics analysis of intestinal contents in Common Carp","description":"To elucidate the metabolic mechanisms underlying the beneficial effects of Enterococcus faecalis on host health under high-carbohydrate-high-fat (HCHF) stress, we performed an untargeted metabolomics analysis on intestinal contents of common carp (Cyprinus carpio). Fish were fed an HCHF diet with or without E. faecalis supplementation (1 x 10^8 CFU/g) for 56 days. After a 24-h fasting, intestinal contents were collected and analyzed using UHPLC-Q-Orbitrap MS in both positive and negative ion modes. Given that E. faecalis significantly enriched the gut beneficial bacterium Cetobacterium somerae, this study aimed to identify key differential metabolites and affected metabolic pathways, and to explore their correlations with the altered microbiota. The results will help uncover the probiotic-host metabolic crosstalk and provide mechanistic insights for aquaculture applications.
","dates":{"publication":"2026-08-09","submission":"2026-08-08"},"accession":"MTBLS15296","cross_references":{}}