Bile Acid Metabolomics – Qualitative Analysis
Qualitative analysis of the mass spectrometry data was performed based on the MWDB (Metware Database), which was constructed using reference standards.
Lipidomics – Qualitative Analysis
Qualitative analysis of lipid species was performed using the built-in MWDB (Metware Database) based on the retention time (RT) and precursor/product ion pair information of the detected compounds.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase","Liquid Chromatography MS - alternating - reverse-phase"],"chromatography_protocol":["Bile Acid Metabolomics – Liquid Chromatography Conditions
Chromatographic separation was performed using a Waters ACQUITY UPLC HSS T3 C18 column (1.8 μm, 100 mm × 2.1 mm i.d.). The mobile phase consisted of A: ultrapure water containing 0.01% acetic acid and 5 mmol/L ammonium acetate, and B: acetonitrile containing 0.01% acetic acid. The flow rate was set at 0.35 mL/min, the column temperature was maintained at 40 °C, and the injection volume was 3 μL. The gradient elution program was as follows: 0 min, A/B = 95:5 (v/v); 1 min, A/B = 60:40 (v/v); 7 min, A/B = 50:50 (v/v); 12 min, A/B = 25:75 (v/v); 14 min, A/B = 5:95 (v/v); and 16.0 min, A/B = 95:5 (v/v).
Lipidomics – Liquid Chromatography Conditions
Chromatographic separation was performed using a Thermo Accucore C30 column (2.6 μm, 2.1 mm × 100 mm i.d.). The mobile phase consisted of A: acetonitrile/water (60:40, v/v) containing 0.1% formic acid and 10 mmol/L ammonium formate, and B: acetonitrile/isopropanol (10:90, v/v) containing 0.1% formic acid and 10 mmol/L ammonium formate. The gradient elution program was as follows: 0 min, A/B = 80:20 (v/v); 2 min, A/B = 70:30 (v/v); 4 min, A/B = 40:60 (v/v); 9 min, A/B = 15:85 (v/v); 14 min, A/B = 10:90 (v/v); 15.5 min, A/B = 5:95 (v/v); 17.3 min, A/B = 5:95 (v/v); 17.5 min, A/B = 80:20 (v/v); and 20 min, A/B = 80:20 (v/v). The flow rate was set at 0.35 mL/min, the column temperature was maintained at 45 °C, and the injection volume was 2 μL.
"],"publication":["Gut microbiota-induced perturbations in bile acids alter keratinocyte lipid metabolism via FXR-NQO1 signaling in psoriasis."],"submitter_name":["Duo Keai"],"submitter_affiliation":["Peking University"],"organism_part":["Serum","Skin"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Bile Acid Metabolomics
For bile acid metabolomics, serum samples were collected from psoriatic mice and psoriasis patients. Briefly, 50 μL of liquid sample was mixed with 2.5 μL of a 10 μg/mL internal standard working solution and 197.5 μL of 20% methanol in acetonitrile. The mixture was vortexed at 2,500 r/min for 10 min and then placed at 20 °C for 10 min. Subsequently, the sample was centrifuged at 12,000 r/min for 10 min at 4 °C, and the supernatant was passed through a protein precipitation plate prior to LC-MS/MS analysis.
Lipidomics
For lipidomics, skin tissue samples were collected from psoriatic mice. Samples were removed from the 80 °C freezer and thawed on ice. After thawing, 20 mg of each sample was weighed into a corresponding 2 mL centrifuge tube. A steel bead was added using forceps, and the sample was homogenized using a ball mill (30 Hz) for 20 s, followed by centrifugation at 3,000 r/min for 30 s at 4 °C to collect the sample at the bottom of the tube (homogenization time could be extended as needed based on the actual homogenization efficiency). Then, 1 mL of lipid extraction solution containing internal standards (methyl tert-butyl ether:methanol = 3:1, v/v) was added, and the mixture was vortexed for 15 min. After adding 200 μL of water and vortexing for 1 min, the sample was centrifuged at 12,000 r/min for 10 min at 4 °C. The supernatant (200 μL) was transferred to a corresponding centrifuge tube and evaporated to complete dryness. Finally, the residue was reconstituted with 200 μL of lipid reconstitution solution (acetonitrile:isopropanol = 1:1, v/v), vortexed for 3 min, and centrifuged at 12,000 r/min for 3 min. The resulting supernatant was used for LC-MS/MS analysis.
"],"organism":["Mus musculus","Homo sapiens"],"data_transformation_protocol":["Bile Acid Metabolomics – Data Processing
Mass spectrometry data were processed using Analyst 1.6.3 software. Based on the retention time and peak shape information of reference standards, chromatographic peaks of target compounds detected in different samples were integrated and calibrated to ensure accurate qualitative and quantitative analysis. Quantitative integration and calibration results across different samples are presented with retention time (min) on the x-axis and ion intensity (cps) on the y-xis. The integrated peak area ratios of all detected samples were substituted into the standard curve linear equation for calculation. After further calculation using the designated formula, the final concentration of each compound in the actual samples was obtained. Notably, the calculation formula includes unit conversion, allowing direct substitution of the corresponding values to determine sample concentrations.
Lipidomics – Data Processing
Mass spectrometry data were processed using Analyst 1.6.3 software. Lipid species in the samples were qualitatively analyzed based on the Metware local lipid database. Subsequently, chromatographic peaks of each lipid species detected in different samples were calibrated to ensure quantitative accuracy. Quantitative integration and calibration results across different samples are presented with retention time (min) on the x-axis and ion intensity (cps) on the y-axis. The integrated peak area ratios of all detected samples were substituted into the linear equation for calculation. After further calculation using the designated formula, the final concentration of each lipid species in the actual samples was obtained. Notably, the calculation formula includes unit conversion, allowing direct substitution of the corresponding values to determine sample concentrations.
"],"study_factor":["Group"],"submitter_email":["keaiduoduo998@126.com"],"metabolights_link":["https://www.ebi.ac.uk/metabolights/MTBLS14191"],"sample_collection_protocol":["For bile acid metabolomics, serum samples were collected from psoriatic mice and psoriasis patients. The skin tissue samples were collected from psoriatic mice. Serum samples and skin tissue were stored at the 80 °C freezer.
"],"omics_type":["Metabolomics"],"study_design":["Gut microbiota","Metabolomics","FXR","AB SCIEX QTRAP 6500+","Mus musculus","SCIEX ExionLC AD","targeted analysis","psoriasis","Keratinocytes","Homo sapiens","Serum","Skin"],"curator_keywords":["Gut microbiota","FXR","Metabolomics","AB SCIEX QTRAP 6500+","Mus musculus","SCIEX ExionLC AD","targeted analysis","psoriasis","Keratinocytes","Homo sapiens","Serum","Skin"],"mass_spectrometry_protocol":["Bile Acid Metabolomics – Mass Spectrometry Conditions
Mass spectrometry analysis was performed using an electrospray ionization (ESI) source. The ion source temperature was set at 550 °C, the ion spray voltage was 4500 V, and the curtain gas (CUR) was maintained at 35 psi. In the triple quadrupole system, each ion pair was monitored using optimized declustering potential (DP) and collision energy (CE).
Lipidomics – Mass Spectrometry Conditions
Mass spectrometry analysis was performed using an electrospray ionization (ESI) source. The ion source temperature was set at 500 °C. The ion spray voltage was 5500 V in positive ion mode and 4500 V in negative ion mode. Ion source gas 1 (GS1) was set at 45 psi, ion source gas 2 (GS2) at 55 psi, and curtain gas (CUR) at 35 psi. In the triple quadrupole system, each ion pair was monitored using optimized declustering potential (DP) and collision energy (CE).
"],"metabolite_name":["cholic acid","apocholic acid","3,7-DIKETOCHOLANIC ACID","7-ketolithocholic acid","Ursocholic acid","Tauroursodeoxycholic acid","ÉÇ-Hyodeoxycholic Acid","12-ketolithocholic acid","3ÉÇ-Cholic Acid","Dehydrocholic acid","Glycochenodeoxycholic Acid 3 Sulfate Disodium Salt","Glycocholic acid","Lithocholic acid","Ursodeoxycholic acid","Isoallolithocholic acid","Taurohyodeoxycholic Acid (sodium salt)","Glycoursodeoxycholic Acid 3 Sulfate Sodium","Àß-muricholic acid","3-Oxocholic acid","lithocholic acid-3-sulfate","Cholic Acid 3 Sulfate Sodium Salt","Deoxycholic Acid 3-O-Sulfate Disodium Salt","3ÉÇ-Glycocholic Acid","taurolithocholic acid-3-sulfate","Chenodeoxycholic acid-3-ÉÇ-D-glucuronide","5Ï«-CHOLANIC ACID-3Ï«-OL","Deoxycholic acid 3,12-disulfate trisodium salt","Ï«-muricholic acid","Taurocholic acid","norcholic acid","Isodeoxycholic acid","ÉÇ-muricholic acid","3ÉÇ-Ursodeoxycholic Acid","3ÉÇ-deoxycholic acid","taurolithocholic acid","Taurohyocholic acid","isolithocholic acid","glycolithocholic acid-3-sulfate","LITHOCHOLENIC ACID","Chenodeoxycholic acid","Taurochenodeoxycholic acid","Chenodeoxycholic acid 24-acyl-b-D-glucuronide","Nor-Deoxycholic Acid","TAUROURSOCHOLIC ACID","Lithocholic Acid 3-O-Glucuronide","7-Ketodeoxycholic acid","hyocholic acid","Taurodeoxycholic acid","Taurodehydrocholic acid","allocholic acid","Tauro-Ï«-muricholicAcid sodium salt","5-ÉÇ-Cholanic Acid-3Ï«-ol-6-one","Dehydrolithocholic acid","cholic acid 7 sulfate","3-oxochenodeoxycholic acid","3ÉÇ-hydroxychol-5-en-24-oic acid","Tauroursodeoxycholic Acid-3-Sulfate Sodium Salt","6,7-diketolithocholic acid","7,12-diketolithocholic acid","12-Oxochenodeoxycholic acid","Glycoursodeoxycholic acid","3,6-DIKETOCHOLANIC ACID","Tauro-Àß-muricholic Acid sodium salt","Cholic Acid 3-O-b-Glucuronide Disodium Salt","Glycochenodeoxycholic acid","12-dehydrocholic acid","Hyodeoxycholic acid","Deoxycholic acid","Glycohyodeoxycholic Acid","Chenodeoxycholic acid 3,7-disulfate trisodium salt","3-oxodeoxycholic acid","Glycohyocholic acid","murideoxycholic acid","Glycolithocholic acid","Glycodeoxycholic acid","Tauro-ÉÇ-muricholic acid","Isochenodeoxycholic Acid","Glycodehydrocholic acid","chenodeoxycholic acid3-sulfate disodium salt","Taurocholic Acid 3 sulfate sodium salt","3-Sulfo-ursodeoxycholic Acid Disodium Salt","Trihydroxycholestanoic Acid"],"additional_accession":[]},"is_claimable":false,"name":"Gut microbiota-induced perturbations in bile acids alter keratinocyte lipid metabolism via FXR-NQO1 signaling in psoriasis","description":"Emerging evidence has shown that microbiota dysbiosis and aberrant bile acids (BAs) profiles are correlated with disease progression. This study elucidates dysregulated BAs metabolism in psoriasis patients and imiquimod-treated female mice, coupled with increased expression of the farnesoid X receptor (FXR) in keratinocytes. Activation of FXR by glycochenodeoxycholic acid (GCDCA) ameliorates psoriatic symptoms by enhancing lipid metabolism, particularly fatty acid oxidation. Mechanistically, the 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