All analytes showed a mass error < 5 ppm and an isotope score > 40 (10 ppm, 90% intensity), meaning that at least the + 1 isotope must be matched.
Analytes containing > 50% missing values in QC samples and study samples and analytes showing > 30% area RSD in matrix specific QC samples were omitted.
Lipids:
MS/MS spectra were matched with a manually curated in-house library cross-checked with MSDIAL-TandemMassSpectralAtlas-VS68-Neg and -Pos.
Polar Metabolites:
MS/MS spectra were matched with mzCloud Omics Offline library version 2020A.
Chromatography Instrument: Thermo Vanquish Horizon
Autosampler Model: Split Sampler HT
Lipidomics (positive and negative reversed-phase metabolites)
Column Model: Zorbax RRHD Eclipse Plus C8 2.1 x 50 mm, 1.8µm (Agilent, Waldbronn, Germany)
Guard Column Model: Zorbax Eclipse Plus C8 2.1 mm, 1.8 µm (Agilent, Waldbronn, Germany)
Column Temperature: 40 °C, flow rate 0.3 mL/min
Solvent A: Water + 0,1 % formic acid + 10 mM ammonium formate
Solvent B: Acetonitrile:isopropanol (2:3) + 0.1% formic acid
14 min binary gradient
Injection Volume positive: 2 µL
Injection Volume negative: 5 µL
Metabolites (positive and negative HILIC metabolites)
Column Model: SeQuant ZIC-HILIC 2.1 x 100 mm 3.5 µm (Merck, Darmstadt, Germany)
Guard Column Model: SeQuant ZIC-HILIC 2.1 x 20 mm Guard Kit (Merck, Darmstadt, Germany)
Column Temperature: 30 °C, flow rate 0.3 – 0.5 mL/min
Solvent A: Water + 0.1% formic acid
Solvent B: Acetonitrile + 0.1% formic acid
26 min binary gradient
Injection Volume positive: 3 µL
Injection Volume negative: 5 µL
"],"publication":["FFAR4-mediated IL-6 release from islet macrophages promotes insulin secretion and is compromised in type-2 diabetes. 10.1038/s41467-025-58706-5. PMID:40210633"],"submitter_name":["Xinyi Chen","Lisa Hahnefeld"],"submitter_affiliation":["Goethe University Frankfurt, Institute of Clinical Pharmacology, Faculty of Medicine, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany","Max Planck Institute for Heart and Lung Research"],"organism_part":["blank","blood plasma","Supernatant"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["- 100 µL of cell supernatant in a 1.5 mL tube (Sarstedt, Nümbrecht, Germany)
+ 75 µL of internal standards solved in methanol
+ 75 µL of methanol
+ 500 µL of MTBE
+ 20 µL of 50 mM ammonium formate solution
- Vortexing for 1 min
- Centrifugation for 5 min at 18,213 x g and 4 °C
- Transfer the upper layer (organic layer) into a glass vial
- Re-extract the lower layer (water layer) with 200 µL MTBE:methanol:water (10:3:2.5, v/v/v, upper layer)
- Vortexing for 1 min
- Centrifugation for 5 min at 18,213 x g and 4 °C
- Combine upper layers and evaporate under a stream of nitrogen at 45 °C (10 min) for lipidomics analysis
- dry lower phase under a stream of nitrogen at 45 °C (20-30 min) for metabolomics analysis
- Store dried samples at < -70 °C until analysis
Post-Extraction: Reconstitute dried organic layer (lipidomics/reversed-phase-metabolites) with 100 µL methanol for the profiling of lipids
Post-Extraction: Reconstitute dried aqueous layer (metabolomics/HILIC metabolites) with 100 µL of acetonitril:water (50:50, v/v)
Solvent Blank: Injection of pure methanol or acetonitril:water (50:50, v/v)
Blank: sample material was replaced with 100 µL of phosphate buffered saline, internal standard was replaced with 75 µL methanol
Zero: sample material was replaced with 100 µL of phosphate buffered saline, 75 µL of internal standard were added
QCZ: Replicates of pooled cell supernatant were extracted as described
QC: Replicates of pooled human plasma (10 µl of sample and 90 µL of 50 mM ammonium formate solution) were extracted as described to verify system stability
"],"organism":["blank sample","Mus musculus","blank","Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS12317"],"author":["Gerd Geisslinger.","Juan Hidalgo.","Zheng Wang.","Stefan Offermanns. Max Planck Institute for Heart and Lung Research, Department of Pharmacology. Max Planck Institute for Heart and Lung Research, Department of Pharmacology, Ludwigstr. 43, 61231 Bad Nauheim, Germany. stefan.offermanns@mpi-bn.mpg.de.","Isabell Brandenburger.","ShengPeng Wang.","Robert Gurke.","Nina Wettschureck.","Xinyi Chen. Max Planck Institute for Heart and Lung Research, Department of Pharmacology. Max Planck Institute for Heart and Lung Research, Department of Pharmacology. Xinyi.Chen@mpi-bn.mpg.de.","Haaglim Cho.","Jingchen Shao.","Rémy Bonnavion.","Lisa Hahnefeld. Institute of Clinical Pharmacology, Goethe University Frankfurt. Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany. hahnefeld@med.uni-frankfurt.de. hahnefeld@med.uni-frankfurt.de.","Weikun Qian."],"data_transformation_protocol":["Data acquisition was carried out using XCalibur v4.4 and the evaluation of raw data was performed using TraceFinder v5.1 (both from Thermo Fisher Scientific). Lipidomics results were normalized using one internal standard per lipid class and polar metabolite results using median-based probabilistic quotient normalization (polarity and sample-wise calculated in R).
"],"study_factor":["Genotype","TUG-891"],"submitter_email":["hahnefeld@med.uni-frankfurt.de","xinyi.chen@mpi-bn.mpg.de"],"sample_collection_protocol":["Mouse pancreatic islets were isolated by collagenase digestion as previously described (Tunaru et al., 2018). In short, islets were prepared from pancreata by collagenase type XI digestion (Sigma, C7657), handpicked, and then incubated in a humidified atmosphere in RPMI 1640 culture medium (Gibco, 21875091) supplemented with 10% (vol/vol) FBS, 100 U/ml penicillin, and 100 U/ml streptomycin. Freshly isolated islets were incubated overnight before the experiment. After the experiments, for the purpose of normalization, islet protein was extracted with RIPA lysis buffer (Thermo Fischer, 89900) and protein level was quantified with the BCA assay (Thermo Fischer, 23227) following the manufacturer’s protocol.
To conduct lipidomic and metabolomic analyses, 10 size-matched islets were taken from each group and were treated in RPMI 1640 culture medium containing 7 mM glucose without or with 20 μM TUG-891 for 48 hrs. Supernatants were collected and subjected to liquid-liquid extraction.
"],"omics_type":["Metabolomics"],"study_design":["cytokine","Mus musculus","blank","untargeted analysis","Supernatant","Homo sapiens","islet macrophages","insulin secretion","Orbitrap Exploris 480","Thermo Scientific Vanquish UHPLC System","blank sample","blood plasma","FFAR4","GPCR","experimental blank"],"curator_keywords":["cytokine","Mus musculus","blank","untargeted analysis","Supernatant","Homo sapiens","islet macrophages","insulin secretion","Orbitrap Exploris 480","Thermo Scientific Vanquish UHPLC System","blank sample","blood plasma","FFAR4","GPCR","experimental blank"],"mass_spectrometry_protocol":["Instrument: Orbitrap Exploris 480 (Thermo Fisher Scientific, Dreieich, Germany)
Ion Source Type: H-ESI
Mass Analyzer: Orbitrap
Scan polarity: positive and negative
Lipidomics (positive and negative reversed-phase metabolites)
Scan m/z range: 180-1500 (positive+negative)
Mass resolution MS1: 120000
Mass resolution MS/MS: 15000
MS/MS Mode: data-dependent (up to cycle time of 0.6 sec)
RF Lens: 25%
Spray Voltage: Static, Positive Ion (V): 3000, Negative Ion (V): 2500
Gas Mode: Static, Sheath Gas (Arb): 40, Aux Gas (Arb): 20, Sweep Gas (Arb): 0
Ion Transfer Tube Temp (°C): 260
Vaporizer Temp (°C): 290
Metabolites (positive and negative HILIC metabolites)
Scan m/z range: 70-700 (positive), 59-590 (negative)
Mass resolution MS1: 120000
Mass resolution MS/MS: 15000
MS/MS Mode: data-dependent (up to cycle time of 0.6 sec)
RF Lens: 20%
Spray Voltage: Static, Positive Ion (V): 3400, Negative Ion (V): 3000
Gas Mode: Static, Sheath Gas (Arb): 25, Aux Gas (Arb): 7, Sweep Gas (Arb): 0
Ion Transfer Tube Temp (°C): 320
Vaporizer Temp (°C): 180
"],"pubmed_abstract":["The function of islet macrophages is poorly understood. They promote glucose-stimulated insulin secretion (GSIS) in lean mice, however, the underlying mechanism has remained unclear. We show that activation of the free fatty acid receptor FFAR4 on islet macrophages leads to interleukin-6 (IL-6) release and that IL-6 promotes β-cell function. This mechanism is required for GSIS in lean male mice, but does not function anymore in islets from people with obesity and obese type 2 diabetic male mice. In islets from obese mice, FFAR4 downstream signaling in macrophages is strongly reduced, resulting in impaired FFAR4-mediated IL-6 release. However, IL-6 treatment can still improve GSIS in islets from people with obesity and obese type 2 diabetic mice. These data show that a defect in FFAR4-mediated macrophage activation contributes to reduced GSIS in type 2 diabetes and suggest that reactivating islet macrophage FFAR4 and promoting or mimicking IL-6 release from islet macrophages improves GSIS in type 2 diabetes."],"pubmed_title":["FFAR4-mediated IL-6 release from islet macrophages promotes insulin secretion and is compromised in type-2 diabetes."],"pubmed_authors":["Chen Xinyi X, Shao Jingchen J, Brandenburger Isabell I, Qian Weikun W, Hahnefeld Lisa L, Bonnavion Rémy R, Cho Haaglim H, Wang ShengPeng S, Hidalgo Juan J, Wettschureck Nina N, Geisslinger Gerd G, Gurke Robert R, Wang Zheng Z, Offermanns Stefan S"],"additional_accession":[]},"is_claimable":false,"name":"FFAR4-mediated IL-6 release from islet macrophages promotes insulin secretion and is compromised in type-2 diabetes","description":"The function of islet macrophages is poorly understood. They promote glucose-stimulated insulin secretion (GSIS) in lean mice, however, the underlying mechanism has remained unclear. We show that activation of the free fatty acid receptor FFAR4 on islet macrophages leads to interleukin-6 (IL-6) release and that IL-6 promotes β-cell function. This mechanism is required for GSIS in lean mice, but does not function anymore in islets from obese type 2 diabetic mice and humans. In islets from obese mice, FFAR4 downstream signaling in macrophages is strongly reduced, resulting in impaired FFAR4-mediated IL-6 release. However, IL-6 treatment can still improve GSIS in islets from obese mice and humans. These data show that a defect in FFAR4-mediated macrophage activation contributes to reduced GSIS in type 2 diabetes and suggest that reactivating islet macrophage FFAR4 and promoting or mimicking IL-6 release from islet macrophages improves GSIS in type 2 diabetes.
","dates":{"publication":"2026-08-19","submission":"2025-03-14"},"accession":"MTBLS12317","cross_references":{"pubmed":["40210633"]}}