Metabolite annotation was performed using the BiotreeDB (V3.0) in-house database, which contains over 20,000 metabolite standards with MS1, MS2, and retention time information. The identification pipeline was implemented in R. Metabolites were matched based on precursor m/z (mass tolerance 15 ppm), retention time (tolerance 0.2 min), and MS/MS fragmentation patterns. Annotation confidence levels followed the Metabolomics Standards Initiative (MSI): Level 1 (authentic standard matching), Level 2 (public library matching), Level 3 (putative annotation), and Level 4 (unknown). The majority of reported metabolites were annotated at MSI Level 2 or higher.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - positive - hilic","Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["Chromatographic separation was performed on a Vanquish UHPLC system (Thermo Fisher Scientific) equipped with a Waters ACQUITY UPLC BEH Amide column (2.1 mm × 50 mm, 1.7 μm particle size). The column temperature was maintained at 40°C. Mobile phase A consisted of 25 mmol/L ammonium acetate and 25 mmol/L ammonia hydroxide in water (pH = 9.75). Mobile phase B was acetonitrile. The flow rate was set to 0.3 mL/min (typical value for this column; exact flow rate as per standard protocol). The injection volume was 2 μL, and the autosampler temperature was kept at 4°C. The gradient program was as follows: 0–2 min, 95% B; 2–11 min, 95–65% B; 11–13 min, 65–40% B; 13–15 min, 40% B; 15–15.1 min, 40–95% B; 15.1–18 min, re-equilibration at 95% B. Total run time was 18 min.
"],"publication":["Non-targeted metabolomics analysis of synovial fluid from TMD patients."],"submitter_affiliation":["Wuhan university"],"submitter_name":["Yong Cheng"],"organism_part":["synovial fluid"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Joint cavity lavage fluid samples (62 experimental samples) were collected and stored at -80°C until processing. For metabolite extraction, 100 μL of each sample was mixed with 400 μL of extraction solution (methanol:acetonitrile = 1:1, v/v) containing deuterated internal standards. The mixture was vortexed for 30 s, sonicated for 10 min in an ice-water bath, and then incubated at -40°C for 1 h to precipitate proteins. After centrifugation at 12,000 rpm (13,800 × g) for 15 min at 4°C, 400 μL of supernatant was transferred to a new tube and dried under vacuum. The dried residue was reconstituted in 100 μL of reconstitution solution (methanol:acetonitrile:water = 2:2:1, v/v/v) containing internal standards, sonicated for 10 min, and centrifuged. The final supernatant was transferred to an autosampler vial for LC-MS analysis. A pooled quality control (QC) sample was prepared by mixing equal aliquots of all experimental sample supernatants. Solvent blanks were also prepared and analyzed throughout the run to monitor carryover.
"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14238"],"author":["Yong Cheng. Wuhan university. wb003142@whu.edu.cn."],"data_transformation_protocol":["Raw mass spectrometry data (.raw files) were converted to mzXML format using ProteoWizard (version 3.0). Peak detection, alignment, and integration were performed using an in-house R package based on XCMS. The resulting data matrix contained peak intensities (area) for all features across all samples. No further normalization was applied at this stage.
"],"study_factor":["Disease status"],"submitter_email":["wb003142@whu.edu.cn"],"sample_collection_protocol":["During Arthrography, 1 mL of sterile saline was injected into the superior joint compartment. Patients performed repeated opening and closing movements to mix the saline with synovial fluid. The mixture was aspirated and re-injected 3–5 times before final collection. Samples were centrifuged at 3,000 rpm for 5 minutes at 4 °C. The supernatant was aliquoted, snap-frozen in liquid nitrogen for 15 minutes, and stored at −80°C.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","pooled quality control sample","Metabolomics","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","synovial fluid","Hydrophobic and Hydrophilic Interactions","Homo sapiens","Articular disc disorder of bilateral temporomandibular joints (disorder)","ProteoWizard msaccess","experimental sample"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","pooled quality control sample","Metabolomics","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","synovial fluid","Hydrophobic and Hydrophilic Interactions","Homo sapiens","Articular disc disorder of bilateral temporomandibular joints (disorder)","ProteoWizard msaccess","experimental sample"],"mass_spectrometry_protocol":["Mass spectrometry was performed using an Orbitrap Exploris 120 mass spectrometer (Thermo Fisher Scientific) equipped with a heated electrospray ion source (HESI). Data were acquired in both positive and negative ion modes in separate runs. For positive ion mode, the spray voltage was set to 3.8 kV; for negative ion mode, spray voltage was set to -3.4 kV. Sheath gas flow rate was 50 Arb, auxiliary gas flow rate was 15 Arb, and capillary temperature was 320°C. Full MS scans were acquired at a resolution of 60,000 (FWHM) over an m/z range of 100–1500. Data-dependent MS/MS scans were performed at a resolution of 15,000 with stepped normalized collision energy (SNCE) of 20/30/40. The acquisition software was Xcalibur (version 4.4, Thermo Fisher Scientific).
"],"metabolite_name":["16-Hydroxypalmitic acid","Allantoin","Embelin","Monomethyl glutaric acid","Prunetin","3,3-Dimethylglutaric acid","3,4-Dihydroxy-phenylalanine","4-Cresol sulfate","Trifluoroacetic acid","8-CHLOROTHEOPHYLLINE","2-Ketocaproic acid","Thiolutin","beta-Alanine","Ketoleucine","Caplamin","Succinate","alpha-Ketoisovaleric acid","(2-aminoethoxy)[3-[hexadec-1-en-1-yloxy]-2-[icosa-5.8.11.14-tetraenoyloxy]propoxy]phosphinic acid","Carprofen","Glycolate","Pentostatin","Capric acid","1-Methylxanthine","1-Hydroxy-2-naphthoic acid","Meglumine","Mesaconic acid","4-Hydroxybenzaldehyde","4-Hydroxyproline","D-myo-Inositol-4-phosphate","Cholesteryl sulfate","Ethacrynic_acid","4,6-Dinitro-o-cresol","7-Hydroxy-3-oxo-cholest-4-en-26-oic acid","Glycine","Gentisic acid","Phosphate","Glutaric acid","Myristoleate","N-Dodecanoyl-N-methylglycine","astilbin","Galactinol","Pseudouridine","Terephthalic-Acid","17-ODYA","Cumate","Pyrogallol","PFOH-perfluoroalkyl_alcoho","2-Hydroxypalmitic acid","Uracil","11-Dehydrocorticosterone","Isovaleric acid","Glyceraldehyde","Ribothymidine","5-Hydroxytryptophol (5HTOL)","5-Aminolevulinic acid","Caprylic acid","Iotalamic acid","4-Methylbenzoic-acid","3-Methylxanthine","3-Methyluridine","Acetylglycine","HEPTANOIC ACID","Glyceric acid","AFMK","5-(4-Hydroxyphenyl)-5-phenylhydantoin","2-amino-3-({[3-(hexadecanoyloxy)-2-(octadecanoyloxy)propoxy](hydroxy)phosphoryl}oxy)propanoic acid","Phthalic acid","2-Arachidonoyl-1-palmitoyl-sn-glycero-3-phosphoethanolamine","12-Methyltridecanoic acid","Pemetrexed","Xylose","2-Imino-1-imidazolidineacetic acid","Oxalic acid","2-amino-3-({hydroxy[2-(icosanoyloxy)-3-(octadecanoyloxy)propoxy]phosphoryl}oxy)propanoic acid","Myristic acid","His-Met","Pyrophosphate","Rhamnose","2-methylglutarate","Uridine","Methylacetate","2-amino-3-({hydroxy[2-(icosanoyloxy)-3-[octadec-11-enoyloxy]propoxy]phosphoryl}oxy)propanoic acid","3-Hydroxybenzoic acid","Methylgallate","Homoserine","4-Hydroxyphenylacetaldehyde","gamma-Linolenic acid","3-Methylthiopropionic acid","(6E)-8-Methyl-6-nonenoic acid","Malonic acid","Hippuric acid","alpha-Linolenic acid","Serine","Proline","Saluamine","risedronate","Isocitric acid","3-Hydroxypropionic acid (beta-lactic acid)","Plumbagin","Gly-Ala","Tetradecyl sulfate (sodium)","5-ketocaproate","N-Lauroylglycine","TRICARBALLYLIC ACID","Glycohyodeoxycholic acid","Glycoursodeoxycholic acid","2-Ethyl-2-hydroxybutyric acid","2-Methylhippuric acid","Pyruvate","2,4-Dihydroxybutanoic acid","Fumaric acid","Heptadecanoic acid","Citraconic acid","2-Arachidonoyl-1-stearoyl-sn-glycero-3-phosphoethanolamine","Lumichrome","Glutamine","2-Amino-3-(1H-pyrazol-1-yl)propanoic acid","Benzoic acid","Dihydroxyacetone","Phenylacetic acid","Sucrose","Caproic acid","1,6-Anhydro-.beta.-D-glucose","Pipamperone","Methylsuccinic acid","Glucose","3-Hydroxyglutaric acid","Palmitic acid","Dodecyl gallate","O-Acetylserine","Ala-Gly","Melibiose","Ethylmalonic acid","1,2-Distearoyl-sn-glycero-3-phospho-L-serine","2-Ketobutyric acid","Isodeoxycholic acid","12-Hydroxydodecanoic acid","Valproic acid","Valeric acid","Nitrofurazone","2-Hydroxystearic acid","Isobutyric_acid","Theophylline","Trehalose","(2E)-4-Hydroxybut-2-enoic acid","Ceftriaxone","Oxacillin","Hydroxyacetone","N-(Dodecanoyl)sphing-4-enine-1-phosphate","myo-Inositol","2,3-Dihydroxybenzoic acid (Pyrocatechuic acid)","Pyroglutamic acid","Xylulose","2,6-Dihydroxybenzoic acid","Salicylic acid","Alanine","Levulinic acid",".alpha.-Hydroxyisobutyric acid","2,2-Dimethylsuccinic acid","3-Methyl-2-oxovaleric acid","Diacetyl","Citric acid","6-Pentyl-2H-pyran-2-one","cis-9-Palmitoleic acid","5-Aminopentanoic acid","Phloroglucinaldehyde","2,4-Dihydroxybenzoic acid","3-Carboxy-4-methyl-5-propyl-2-furanpropanoic_acid","Syringic_acid","2-Anilinopropanoic acid","Hydroxyisocaproic acid","Lactate","cis-9,10-Epoxystearic acid","Theobromine","2-Hydroxyhexanoic acid","Glycocholic acid","Ursodeoxycholic acid","Isocaproic acid","Itaconic acid","Perfluoropropanoic acid","3-Hydroxypyruvic acid","Maleic acid","Malic acid","(2-aminoethoxy)[2-[docosa-4.7.10.13.16.19-hexaenoyloxy]-3-[hexadec-1-en-1-yloxy]propoxy]phosphinic acid","Stearic acid","Docebenone","1-Stearoyl-2-arachidonoyl-sn-glycero-3-phospho-(1'-myo-inositol)","7-Methylxanthine","(4S,5Z,6S)-4-(2-methoxy-2-oxoethyl)-5-[2-[(E)-3-phenylprop-2-enoyl]oxyethylidene]-6-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4H-pyran-3-carboxylic acid","Androsterone sulfate","3-Amino-4-methylpentanoic acid","Indoxyl sulfate","1,2-Di(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphoethanolamine","Glyco-gamma-muricholic acid","2-Hydroxy-2-methylbutyric acid","DL-Isocitric acid lactone","Pyruvaldehyde","12-Hydroxystearic acid","Genistein","Parabanic acid","Dodecanoic acid","4-Hydroxyphenylpyruvic acid","4-Aminobutyric acid (GABA)","10-Hydroxydecanoic acid","Ribose","Lorazepam glucuronide","Gallate","cis-Aconitic acid","2-Linoleoyl-1-palmitoyl-sn-glycero-3-phosphoethanolamine","Tartaric acid","Pelargonic acid","Piscidic_Acid","Deoxycholic acid","Hyodeoxycholic acid","2,4-Pyrimidinediamine, 5-[[3-methoxy-4-[(4-methoxyphenyl)methoxy]phenyl]methyl]-","Sarcosine","Glycodeoxycholic acid","Galactose","N-Acetylalanine","1,7-Dimethylxanthine"],"additional_accession":[]},"is_claimable":false,"name":"Non-targeted metabolomics analysis of synovial fluid from TMD patients","description":"This study performed non-targeted metabolomics detection on 62 human joint cavity lavage fluid samples using UHPLC-QE-MS. Metabolites were extracted with methanol:acetonitrile (1:1), separated on a Waters ACQUITY UPLC BEH Amide column, and detected by Orbitrap Exploris 120 mass spectrometer in both positive and negative ion modes. Data were processed using XCMS-based in-house R package and annotated against BiotreeDB (V3.0).","dates":{"publication":"2026-09-23","submission":"2026-04-08"},"accession":"MTBLS14238","cross_references":{"HMDB":["HMDB0000716","HMDB0000050","HMDB0000699","HMDB0000875","HMDB0000089","HMDB0000157","HMDB0032538","HMDB0060656","HMDB0000452","HMDB0004988","HMDB0240288","HMDB0000824","HMDB0004827","HMDB0000172","HMDB0000736","HMDB0062203","HMDB0000086","HMDB0013127","HMDB0000883","HMDB0000251","HMDB0033951","HMDB0002721","HMDB0001934","HMDB0000301","HMDB0001906","HMDB0006695","HMDB0000062","HMDB0001252","HMDB0000097","HMDB0014416","HMDB0000562","HMDB0249241","HMDB0000034","HMDB0004193","HMDB0002013","HMDB0032055","HMDB0060741","HMDB0000043","HMDB0002366","HMDB0061115","HMDB0061822","HMDB0001406","HMDB0003243","HMDB0011749","HMDB0251526","HMDB0002141","HMDB0094696","HMDB0030396","HMDB0000159","HMDB0013128","HMDB0000195","HMDB0000819","HMDB0012108","HMDB0013337","HMDB0005923","HMDB0004366","HMDB0256256","HMDB0094708","HMDB0062769","HMDB0014426","HMDB0000688","HMDB0246162","HMDB0013130","HMDB0000201","HMDB0246950","HMDB0000756","HMDB0010407","HMDB0041922","HMDB0245025","HMDB0000182","HMDB0004620","HMDB0000925","HMDB0004437","HMDB0000791","HMDB0240585","HMDB0061384","HMDB0004194","HMDB0000148","HMDB0000092","HMDB0011506","HMDB0000651","HMDB0002038","HMDB0001539","HMDB0001565","HMDB0010379","HMDB0243890","HMDB0010386","HMDB0002250","HMDB0035248","HMDB0035289","HMDB0031849","HMDB0000564","HMDB0246517","HMDB0243946","HMDB0001538","HMDB0001325","HMDB0000214","HMDB0031641","HMDB0061712","HMDB0000660","HMDB0010390","HMDB0015101","HMDB0000517","HMDB0000479","HMDB0000177","HMDB0000064","HMDB0006344","HMDB0010381","HMDB0062559","HMDB0036584","HMDB0000039","HMDB0246022","HMDB0005066","HMDB0013222","HMDB0007869","HMDB0008097","HMDB0000222","HMDB0010384","HMDB0259112","HMDB0007972","HMDB0014642","HMDB0008031","HMDB0000593","HMDB0007982","HMDB0251355","HMDB0000306","HMDB0002730","HMDB0000197","HMDB0014581","HMDB0250838","HMDB0039531","HMDB0250712","HMDB0000167","HMDB0014634","HMDB0008994","HMDB0008038","HMDB0061680","HMDB0002064","HMDB0004350","HMDB0010382","HMDB0000870","HMDB0061705","HMDB0001097","HMDB0000323","HMDB0014984","HMDB0252136","HMDB0000256","HMDB0244082","HMDB0062225","HMDB0031654","HMDB0029412","HMDB0254880","HMDB0031642","HMDB0341243","HMDB0015319","HMDB0012101","HMDB0243891","HMDB0011253","HMDB0259165","HMDB0008039","HMDB0002201","HMDB0034301","HMDB0012242","HMDB0251214","HMDB0010395","HMDB0007921","HMDB0302581","HMDB0041945","HMDB0256439","HMDB0002166","HMDB0253644","HMDB0012107","HMDB0003012","HMDB0243942","HMDB0012296","HMDB0037822","HMDB0029586","HMDB0243828","HMDB0008002","HMDB0007973","HMDB0039528","HMDB0013409","HMDB0011262","HMDB0242151","HMDB0007991","HMDB0061716","HMDB0013679","HMDB0244231","HMDB0030285","HMDB0015334","HMDB0242561","HMDB0246412","HMDB0014797","HMDB0060655","HMDB0029531","HMDB0241157","HMDB0011352","HMDB0241684","HMDB0035359","HMDB0245026","HMDB0032231","HMDB0030352","HMDB0033871","HMDB0014550","HMDB0005779","HMDB0008727","HMDB0041965","HMDB0251169","HMDB0304156","HMDB0013238","HMDB0240766","HMDB0241377","HMDB0241483","HMDB0241541","HMDB0240750","HMDB0241215","HMDB0244975","HMDB0341357","HMDB0012897","HMDB0241710","HMDB0013329","HMDB0011180","HMDB0241744","HMDB0250739","HMDB0240687","HMDB0037781","HMDB0258887","HMDB0013161","HMDB0241110","HMDB0029416","HMDB0039834","HMDB0015224","HMDB0003148","HMDB0008443","HMDB0006317","HMDB0014331","HMDB0061189","HMDB0029579","HMDB0035762","HMDB0007956","HMDB0035360","HMDB0032304","HMDB0033453","HMDB0030775","HMDB0002249","HMDB0014618","HMDB0014494","HMDB0253763","HMDB0035508","HMDB0008127","HMDB0061007","HMDB0008126","HMDB0012135","HMDB0243790","HMDB0037510","HMDB0031237","HMDB0008753","HMDB0038561","HMDB0014643","HMDB0031292","HMDB0246202","HMDB0251894","HMDB0015227","HMDB0030670","HMDB0038811","HMDB0037204","HMDB0014526","HMDB0029606","HMDB0015090","HMDB0034910","HMDB0253427","HMDB0014917","HMDB0037956","HMDB0030008","HMDB0032737","HMDB0259890","HMDB0008330","HMDB0008338","HMDB0010402","HMDB0007994","HMDB0244825","HMDB0008074","HMDB0008707","HMDB0010383","HMDB0240262","HMDB0008391","HMDB0008751","HMDB0246913","HMDB0012097","HMDB0038658","HMDB0008361","HMDB0008653","HMDB0008235","HMDB0012103","HMDB0008461","HMDB0008066","HMDB0008244","HMDB0015153","HMDB0256988","HMDB0114827","HMDB0115149","HMDB0041540","HMDB0038841","HMDB0008334","HMDB0007075","HMDB0010385","HMDB0010404","HMDB0008363","HMDB0007955","HMDB0252724","HMDB0031802","HMDB0002326","HMDB0012285","HMDB0008509","HMDB0031235","HMDB0038183","HMDB0013631","HMDB0252956","HMDB0302534","HMDB0037382","HMDB0014572","HMDB0014707","HMDB0014405","HMDB0011678","HMDB0240478","HMDB0304781","HMDB0254481","HMDB0014648","HMDB0251870","HMDB0013929","HMDB0014672","HMDB0030201","HMDB0256598","HMDB0005788","HMDB0014455","HMDB0252265","HMDB0014844","HMDB0258335","HMDB0030246","HMDB0030688","HMDB0010388","HMDB0015484","HMDB0015386","HMDB0015195","HMDB0015196","HMDB0010392","HMDB0036440","HMDB0014886","HM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