MassIVEapplication/xmlftp://massive.ucsd.edu/v07/MSV000094355/primaryOK200ProteomicsMarkus Rinschen6495C Triple Quadrupole LC/MSHumanhttps://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=47883b17d55b400f89eeba94c6e6cf8drinschen@biomed.au.dkaarhus UniversityMassIVE54MS:1002864 - No post-translational-modifications are included in the identified peptides of this datasetWater, sodium salt, SPI3, ammonium formate, 13C-labeled, IL1BC, MeCN, cadmium salt, ion, Raw, SMC3, Smc3, CASP-1, H(2)O, BOUND WATER, chronic obstructive pulmonary disease (COPD), Metabonomics, magnesium formate, oxidane, zinc salt, WATER, HOH, l(1)AA33, 5730420M11Rik, dmTAF[[II]]230, T22F8_160, cobalt(II) formate dihydrate, ATGPR7, CH3-C#N, High Performance Liquid Chromatography, Chronic irreversible airway obstruction, 1, methylenesuccinic acid, GRP8, 2, GRP7, germacrene A synthase activity, Analysis, Faroe Islands, Il1bc, WMS, 2310065E01Rik, HACD1, SET, C, 2810441M03Rik, Divorced, TFIID TAF250, Dlp1, Analyses, cel, M, itaconic acid, CAFL - Chronic airflow limitation, HardwareType, Divorces, IL-1BC, HPLC, AI047805, DmelCG4299, PA1, MCAP, DmelCG9748, set, column, BEL, Bel, l(1)B2/13.1, disease (COPD), sample, Chromatography, high pressure, 4732490P18Rik, High Speed Liquid, DmAAF34715, Smcd, nickel salt, SGS, LC-MS2, SH3P12, chronic obstructive lung disease [Ambiguous], dTAF[[II]]230, l(1)LB9, DmRH6, Viral, Caspase-1 subunit p10, cobalt (+2) salt, Liquid Chromatography, TAF200, acu, SORB1, anon-85Ab, ms(3)neo30, Spectrum Analysis, not genetically inherited, DmelCG7788, ACMICD, CHRONIC OBSTRUCTIVE AIRWAY DIS, H2O, sodium (4:1:1) salt, Dm1, magnesium salt, actin, Ag 72H5, Airflow Obstruction, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, Hydrogen Oxide, Act57A, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, Chronic obstructive lung disease, CG33979, HLA-DR-associated protein II, instrument, DI-2, I-2Dm, disodium salt, formate, Spectrometry, cromium (+3), Controls, Rexin, Act57b, I-2PP1, Speed, TAF-IBETA, F2G1.4, Taf250, OBSTRUCTIVE PULMONARY DISEASE (COPD), spirit of wood, liquid chromatography-tandem mass spectroscopy, Drice, ammonium (4:1) salt, DCAP, TAF-Ibeta, disease characteristic, methyl cyanide, DmelCG18408, DRICE, lead (+2) salt, Methyl Alcohol, TAF230, gp160, Dnmlp1, nickel formate dihydrate, lead formate, DrIce, DrICE, l(3)L4740, aluminum salt, CAO - Chronic airflow obstruction, secondary metabolites, 2-trans, CH3OH, CG4795, CHRONIC OBSTRUCTIVE PULM DIS, Chronic obstructive pulmonary disease NOS, NAT13P, Chalk, and RNA binding 1, CG7826, agua, Chronic obstructive pulmonary disease finding, DmelCG9802, CG30294, python, PULMONARY DISEASE (COPD), c-Cbl-associated protein, capping protein, LC-MSMS, Dcap, CG7835, SH3 domain protein 5, CG42273, qualifier, nat13, Boas, CAP1-PEN, anatomical systems, dTAF[[II]]250, PI-6, methylidenebutanedioate, thallium (+1) salt, cell, Placental thrombin inhibitor, PCE-2, rubidium salt, 2pp2a, Act57, methanoic acid, ions, High-Performance Liquid Chromatographies, PI6, BMH, CG10574, Viral Inactivation, Solution, CD156, dTAF250, Faeroe Islands, Quality Controls, 2PP2A, L3, Caspase-1 subunit p20, ATGRP7, ATGRP8, NEC, dSET, dSet, Chronic, T10, itaconate, CG3451, UPLC, CSPG6, LB5, modifier, 1-(14)C-labeled, chronic obstructive airways disease NOS, caspase 3, Inactivation, mak3, COAD, CG9802, Methyl alcohol, Boa, BG:DS00004.13, potassium formate, CE-2, copper (+2) salt, Rnt, COLD - Chronic obstructive lung disease, acetonitrile, Qualifier, (+)-(10R)-germacrene A synthase activity, buffer, Cell, chronic, Cytoplasmic antiproteinase, dTAF230, cpn, lLB5, DmelCG4795, MS, Temperatures, I-2PP2A, cupric formate, chemical analysis, Dm I-2, 9530001P15Rik, TAF[[II]]250/230, MFS1, Sodium, MeOH, (COPD), chronic airway obstruction, chronic obstructive, aluminum formate, CAL - Chronic airflow limitation, Mass Spectrum Analyses, disease qualifier, Mab77H5, Taf[[II]]250, AU020952, Cyclic ADP-ribose hydrolase 1, lithium formate, Col4a-1, ensemble, Separations, GR-RBP7, GR-RBP8, metabolite, DmelCG33979, IL-1 beta-converting enzyme, ethanenitrile, Interleukin-1 beta-converting enzyme, CD156a, FLAF2, 6330417M19Rik, SH3D5, Modifier, ME-IV, HUNKI, High Pressure, chronic obstructive lung disease (disorder), Sh3d5, liquid chromatography tandem mass spectrometry, [OH2], Mak3, HUNK1, l(2)06955, Data Analyses, Methoxide, chronic obstructive pulmonary disease, MAK3, liquid chromatography tandem mass spectroscopy, IPP2A2, Bru, T22F8.160, Meth, NCMe, determination, and rna binding 2, Anaconda, I-19, Chronic Airflow Obstructions, leg, instrument configuration, Metabonomic, zinc formate, CG7788, crice, atado, lead salt, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase, primary metabolites, ammonium tetraformate, chronic obstructive airways disease NOS (disorder), Virus, l(3)S097074, Min, cg9748, Chronic Obstructive Pulmonary Disease (COPD), cADPr hydrolase 1, DmelCG42273, wood alcohol, Mass Spectrum Analysis, Svc, COLD (chronic obstructive lung disease), LCMSMS, NEC in ICD9CM_2006, TAF-I, punc, E430039A18Rik, min, mAPC, CG12352, copper, Mmip1, Chronic airflow limitation, hNAT5, IGAAD, DmSMC3, reaction, lithium salt, High-Performance, hSAN, DmelCG10574, ICE, Ice, GLYCINE RICH PROTEIN 7, RUN, Run, C16orf53, dihydridooxygen, ms(3)Pneo85A, High-Performance Liquid, Sodium Methoxide, dihydrogen oxide, glycine-rich RNA-binding protein 8, GPHYSD2, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, ammonium (2:1) salt, Mak3p, CHRONIC, phapii, (+)-germacrene A synthase activity, NIM-R5 antigen, obstructive lung disease, Alcohol, iCE, ice, NAT13, drice, aqua, LC-MS/MS, Dmel_CG7826, StF-IT-1, cyclase-associated protein, TAFII-250, CD38, TAF250/230, Ponsin, Nat13, Airflow Obstructions, AA33, Multiple Reaction Monitoring, Spectroscopy, pulmonary disease (COPD), TAFII250, Ionen, drIce, drICE, CG5061, CHRONIC OBSTRUCTIVE, chronic obstructive pulmonary disease and allied conditions, Chronic airway disease, NOS, Peptidase inhibitor 6, GAS, nickel (+2) salt, Carbinol, Dmel_CG7835, CG10067, COPD NOS, Crystal, carbinol, CHRONIC OBSTRUCTIVE LUNG DIS, Mnb, MNB, Chronic airway obstruction, ammonium salt, PTI, psi, cold, CAP/Vinexin, MS/MS, Drp1, P45, CG9748, hydrogen hydroxide, Control, cobaltous formate, Actin, Quality, DmSMC3/Cap, CG4299, MASS, AW124434, CG17603, TAF[[II]], acqua, Chronic Airflow Obstruction, data analysis, Wood, 2'-phospho-ADP-ribosyl cyclase|2'-phospho-cyclic-ADP-ribose transferase, COPD - Chronic obstructive pulmonary disease, SR3-5, metabolites, copper salt, chronic obstructive airways disease, p45, Liquid, SMC3L1, Wasser, obstructive pulmonary disease (COPD), i2pp2a, chronic obstructive lung disease, COLD, 2600005K24Rik, rexin, Ag72H5, 2010309L07Rik, AI450666, act57b, ADPRC 1, CG1849, vp165, d230, nat5, DISEASE (COPD), PLAP, cesium salt, FBN, Methyl, dTAFII250, NAT5P, Anacondas, circadian rhythm, Spectrum Analyses, Methylalkohol, EfW1, anon-EST:CL2c12, Boinae, Capt, PHAPII, LC-MS-MS, hardware, Buffer, formic acid, act57B, act57A, Cold, dSMC3, potassium salt, Pulmonary Disease, dmTAF1, Taf230, ECTOL1, 14C-labeled, 2'-phospho-cyclic-ADP-ribose transferase, Tina, Mass, mKIAA1296, Wood Alcohol, Del(8)44H, Metabolomic, Separated, IRAP, Mass Spectroscopy, TAF250, Cold Temperatures, Taf200, DFNB91, Glass, R85FL, DmelCG10067, MRM, CG5074, iones, MS2, Runt, ipp2a2, Taf1p, MSTP057, eau, calcium formate, Chronic Obstructive, OCTD, data processing, wood naphtha, taf-ibeta, statistical analysis., DmelCG12352, NAT5, Nat5, Ultra Performance Liquid Chromatography, 3.2.2.6, methylenebutanedioic acid, cromium (+3) salt, TAF, sodium formate, COPD, High-Performance Liquid Chromatography, span, 2'-phospho-ADP-ribosyl cyclase, 2.4.99.20, COAD - Chronic obstructive airways disease, DYRK1, TAF[[II]]250, nickel formate, 3H-labeled, D16H22S680E, not elsewhere classified, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, DmelCG1849, igaad, strontium formate, l(3)84Ab, l(3)S047110, strontium salt, BEST:RE38067, PULM DIS CHRONIC OBSTRUCTIVE, Chronic obstructive pulmonary disease finding (finding), group, Python, AW112078, LC/MS/MS, cyclic ADP-ribose hydrolase 1, p230, water, I2PP2A, TFIID, CAP, Cap, Dyrk1, CES2A1, GLYCINE-RICH RNA-BINDING PROTEIN 7, BG02184, ACETONITRILE, tandem MS, cyanomethane, WMS2, chronic obstructive airway disease, SAN, San, Temperature, Mass Spectrum, Separation, TAF[[II]]230, l(3)85Ac, Dops, act 57A, CC1, cap, 77H5, TAF[II]250, l(1)19Ea, BcDNA:LD24380, sample population, chromic formate, Interleukin-1 beta convertase, P235, san, dSET/TAF-Ibeta, CG18409, 2610030F17Rik, DmelCG17603, CG18408, Ion, Data, wood spirit, Acap, BAM, SSKS, 3.4.22.36, l(3)L3, calcium salt, cold (chronic obstructive lung disease), High Performance Liquid, Chronic Obstructive Lung Disease, assay, Pythons, AA407739, ADP-ribosyl cyclase 1, TAF1Cell., Profiles, Metabolic, Metabolic Profile, Metabolomes, Profile, Metabolic ProfilesfalseEffect of itaconate and 4-octylitaconate on the metabolome of VSV infected cellsMetabolites extraction. Metabolites were extracted from cells on ice using 800 ul 100% methanol for viral inactivation, followed by 200 ul of ice cold HPLC-grade water. The cell solutions were vortexed for 10 seconds and incubated at -20 degrees C for 2 h. Then, the cell solutions were centrifuged at 4 degrees C, 16 000 g for 20 min, and the supernatants were transferred to 1.5 ml Eppendorf tubes. The supernatants were dried down in a speedvac (Labconco Centrivap) at 8oC. The dried metabolite extracts were resuspended in 100 ul of acetonitrile-water (1:1, v/v) and sonicated for 10 min in ice water. The solution was centrifuged at 4 degrees C, 16 000 g for 20 min. The supernatants were transferred to a 96-well plate (Greiner) and were subjected to targeted metabolomics LC-MS/MS analysis using a list of known itaconate-related metabolites. A quality control sample was prepared by pooling together 5ul of all samples and was used to observe the instrument performance during the run. Targeted metabolomics analysis and mass spectrometry. Targeted metabolomic analysis was performed on a triple quadrupole (QQQ) mass spectrometer (Agilent Triple Quadrupole 6495C, San Diego, CA), coupled to an ultra-high pressure liquid chromatography system (UPLC) system (1290 Infinity, Agilent Technologies) as previously described 81. Data were acquired with Agilent MassHunter Workstation Data Acquisition (version 10.1). A CSH Phenyl-hexyl column (1.7 um, 1.0 x 100 mm) (Waters, Taastrup, Denmark) was used for metabolites separation. Collision energies and product ions (MS2 or quantifier and qualifier ion transitions) were optimized. Electrospray ionisation source conditions were set as follows: gas temperature, 200 degrees C; gas flow, 15 L/min; Nebulizer, 25 psi; sheath gas temperature, 325 degrees C; cap voltage, 3000 V; and nozzle voltage, 500 V. For the liquid chromatography, the following parameters were used. The gradient consisted of buffer A, and buffer B. Buffer A was 99.9% H2O and 0.1% formic acid. Buffer B was 99.9% acetonitrile and 0.1% formic acid. The gradient with A/B ratios were as follows: T0, 99:1; T2.5, 99:1; T6, 86.9:13.10; T7, 1:99; T8.5, 1:99; T9, 99:1; T10, 99:1. The flow rate was 150ul/min. Three microliters of sample were injected. Multi reaction monitoring (MRM) was used. A standard curve was recorded and integrated using the mass hunter platform (Agilent). The transitions used for 4-octyl-itaconic acid were 241.14 -> 111 (quantifier, collision energy - 12 V), 241.14 -> 67.1 (qualifier, collision energy - 24 V). The transitions for itaconic acid were the following: 129.02 -> 85.1 (quantifier, collision energy - 8 V), 129.02 -> 41.2 (qualifier, collision energy - 12 V). Retention time for 4-octyl itaconic acid was 8.2 min, and 2.0 min for itaconic acid. Targeted metabolomics data analysis. Transition lists, retention time and raw data were loaded into Skyline (version 23.1) 82. Then, peaks were evaluated and integrated, and intensities were exported. The area under the curve of the quantifiers was used for further analysis. Data were plotted using python v3.9 83 , and the packages matplotlib v3.5.1, numpy v1.22.2 83, pandas v1.4.1, seaborn v0.12.0, statannotations v0.4.4. T-test independent was used for statistical analysis.Tue Mar 19 02:37:00 GMT 2024MSV0000943559606