The online KEGG, HMDB database was used to annotate the metabolites by matching the exact molecular mass data (m/z) of samples with those from database. If a mass difference between observed and the database value was less than 10 ppm, the metabolite would be annotated and the molecular formula of metabolites would further be identified and validated by the isotopic distribution measurements. We also used a in-house fragment spectrum library of metabolites to validate the metabolite identidification.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse phase","Liquid Chromatography MS - positive - reverse phase"],"chromatography_protocol":["All samples were acquired by the LC-MS system followed machine orders. Firstly, all chromatographic separations were performed using a Thermo Scientific UltiMate 3000 HPLC. An ACQUITY UPLC BEH C18 column (100 mm x 2.1 mm, 1.8 μm, Waters, UK) was used for the reversed phase separation. The column oven was maintained at 35 °C. The flow rate was 0.4 mL/min and the mobile phase consisted of solvent A (water, 0.1% formic acid) and solvent B (acetonitrile, 0.1% formic acid). Gradient elution conditions were set as follows: 0.0-0.5 min, 5% B; 0.5-7.0 min, 5-100% B; 7.0-8.0 min, 100% B; 8.0-8.1 min, 100-5% B; 8.1-10.0 min, 5% B. The injection volume for each sample was 4 μL.
"],"publication":["Caffeine Enhances Antitumor T-cell Activity via COL12A1/IDO1/Kyn axis and Sensitivity to Anti-PD-1 Immunotherapy in Colorectal Cancer."],"submitter_name":["Yuechen Liu"],"submitter_affiliation":["Southern Medical University"],"organism_part":["HCT-116 cell"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["The collected samples were thawed on ice, and metabolite were extracted with 50% methanol buffer. Briefly, 20 μL of sample was extracted with 120 μL of precooled 50% methanol, vortexed for 1 min and incubated at room temperature for 10 min; the extraction mixture was then stored overnight at -20 °C. After centrifugation at 4000 x g for 20 min, the supernatants were transferred into new 96-well plates. The samples were stored at -80 °C prior to the LC-MS analysis. In addition, pooled QC samples were also prepared by combining 10 μL of each extraction mixture
"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS11623"],"author":["Liu Yuechen. lyc19960908@163.com."],"data_transformation_protocol":["The acquired MS data pretreatments including peak picking, peak grouping, retention time correction, second peak grouping, and annotation of isotopes and adducts was performed using XCMS software. LC-MS raw data files were converted into mzXML format and then processed by the XCMS, CAMERA and metaX toolbox implemented with the R software.
"],"study_factor":["caffeine"],"submitter_email":["lyc19960908@163.com"],"sample_collection_protocol":["Supernatants from caffeine-treated and untreated HCT116 tumor cells
"],"omics_type":["Metabolomics"],"study_design":["Caffeic Acids","untargeted metabolites","culture supernatant"],"curator_keywords":["Caffeic Acids","untargeted metabolites","culture supernatant"],"mass_spectrometry_protocol":["A high-resolution tandem mass spectrometer Q-Exactive (Thermo Scientific) was used to detect metabolites eluted form the column. The Q-Exactive was operated in both positive and negative ion modes. Precursor spectra (70-1050 m/z) were collected at 70,000 resolution to hit an AGC target of 3e6. The maximum inject time was set to 100 ms. A top 3 configuration to acquire data was set in DDA mode. Fragment spectra were collected at 17,500 resolution to hit an AGC target of 1e5 with a maximum inject time of 80 ms. In order to evaluate the stability of the LC-MS during the whole acquisition, a quality control sample (pool of all samples) was acquired after every 10 samples.
"],"metabolite_name":["Caffeoyl tyrosine","Doxazosin","2-Furoate","Olanzapine","Corticosterone","11,12-Dimethoxydihydrokawain","Salmeterol","4-(4-Hydroxyphenyl)-2-butanone","Methionine sulfoximine","Diazoxide","Piceatannol","Folic acid","Petunidin 3-glucoside","Cefuroxime","Deoxyinosine","(2-Naphthalenyloxy)acetic acid","Deoxyribose 1-phosphate","Pantothenol","Indole-3-methyl acetate","Ergonovine","L-Erythrulose","Ketoleucine","Cyanidin 3-sambubioside 5-glucoside","Thalidomide","Tetracosanoic acid","Isosakuranin","Paraoxon","3-Methyl-3-hydroxypentanedioate","Biotin","[4]-Gingerdiol 3,5-diacetate","Scopoletin","Carprofen","Paxilline","Capric acid","1-Methylxanthine","Terephthalate","(S)-Isocorydine","4-tert-Butylphenol","Ampicillin","Pentobarbital","Amlodipine","Neopterin","Thiazole","Cyclohexane-1-carboxylate","Lamotrigine","Cefoperazone","1-Hexadecanol","Histidinyl-Serine","Valaciclovir","Glechomafuran","9-cis-Retinoic acid","Methylglutaric acid","Estradiol","Agnuside","Ureidopropionic acid","Lusitanicoside","Perfluorooctanoic acid","Oleic acid","Secobarbital","Aflatoxin G2","Boldione","Aflatoxin G1","Epsilon-(gamma-Glutamyl)-lysine","D-Glyceric acid","12,13-DHOME","2,4,12-Octadecatrienoic acid isobutylamide","Miglitol","Uridine diphosphate-N-acetylglucosamine","Lamivudine","Glycitein","4-Coumarate","Fexofenadine","Sulfisoxazole","Pentazocine","4-Hydroxybenzeneacetonitrile","Homovanillate","3-(2-Hydroxyphenyl)propanoic acid","Triclosan","Imidacloprid","Ciprofloxacin","Acifluorfen","Pantothenic acid","4-Pyridoxic acid","1H-Indole-3-carboxaldehyde","Yohimbine","D-Glucurono-6,3-lactone","Guanosine","Sinapyl alcohol","Ascorbate","beta-D-Glucosamine","Doxorubicin","Myricetin","ADP","D-Glucosamine 6-phosphate","Shikimic acid","Cryptochlorogenic acid","Malabaricano","1,3,7-Trimethyluric acid","3-Oxocholic acid","Metaproterenol","Saccharin","alpha-Mangostin","3-Methylxanthine","3-hydroxytetradecanoic acid","Sulfadoxine","Glyceric acid","Flurbiprofen","Pyridoxamine 5'-phosphate","Loteprednol","Crustecdysone","Phthalic acid","Deoxyribose 5-phosphate","Cyclic AMP","5-Methoxytryptamine","Mupirocin","Prostaglandin D3","cis-Aconitate","4-Bromophenol","2-Phosphoglyceric acid","Isorhamnetin","Sulfamethazine","Oxalacetic acid","Raloxifene","1,3-Benzenediol","Bendroflumethiazide","Enterodiol","Cefalotin","Sulfaquinoxaline","3-Methyladenine","D-Glucose","Juglone","Dantrolene","Gentisate aldehyde","Glucobrassicin","Isoeugenol","6''-O-p-Coumaroyltrifolin","3-Hydroxymethylglutaric acid","Tridecanoic acid","Thiopental","6-Keto-prostaglandin F1a","Cyanidin 3-glucoside","Sulfasalazine","13-OxoODE","Probenecid","Methazolamide","Estrone sulfate","Desmethylxanthohumol","2,3,6-Trimethylphenol","Prostaglandin B1","PA(16_0_16_0)","Indolepyruvate","3-O-Acetylepisamarcandin","Macrocarpal B","Guanidoacetic acid","Isoquercitrin","Rutarin","Acitretin","L-Tyrosine","Matairesinol","L-Dopa","Aflatoxin B2","Digalacturonate","D-Erythrose 4-phosphate","1,5-Anhydro-D-glucitol","Glucoiberin","20-Carboxy-leukotriene B4","Melatonin","5a-Tetrahydrocortisol","Daidzin","Sucrose","3-Hydroxycapric acid","Acoric acid","D-Ribulose 5-phosphate","Cinolazepam","Methylsuccinic acid","Clomipramine","Hydantoin-5-propionic acid","Docosahexaenoic acid","Alpha-dihydroartemisinin","3-Hydroxyanthranilate","(-)-Jasmonic acid","Phloretin","Spermidine","Metosulam","Minocycline","Glucoraphanin","(R)-Mevalonate","CMP","Terephthalic acid","Ribitol","L-Iditol","Luteolin 7-galactoside","Nitrofurazone","Dehydroepiandrosterone sulfate","Buprenorphine","L-Cystathionine","Acetaminophen","Amoxicillin","Perindopril","Lupulone","Indolebutyric acid","Docosapentaenoic acid (22n-3)","4-Acetylbutyrate","Trehalose","Cefradine","Suberic acid","Avicularin","Galactonic acid","Ceftriaxone","3-Methoxyanthranilate","Uridine diphosphategalactose","2-Arachidonylglycerol","Gancaonin A","Dichlorphenamide","m-Cresol","D-Fructose 1-phosphate","Prednisolone","2',5'-Dihydroxychalcone","Creatinine","Coniferin","Citicoline","dGMP","Xanthosine","5-[(E)-2-(4-hydroxy-3-methoxyphenyl)ethenyl]benzene-1,3-diol","(R)-(E)-Sulforaphene","n-Propyl gallate","Citric acid","Nafcillin","(-)-Epicatechin 3-O-gallate","7-Methylguanine","Sulfamethizole","Cefazolin","5-Aminopentanoic acid","Carboxy-ibuprofen","12-KETE","Aesculin","Glycyl-leucine","Dihydrobiopterin","Cefotaxime","4-Aminosalicylate","Isochlorogenic acid b","Levonorgestrel","trans-3-Hydroxycinnamate","Theobromine","Lirioresinol A","alpha-D-Ribose 1-phosphate","Quercetin 3-glucosyl-(1->2)-galactosyl-(1->2)-glucoside","Milrinone","Pravastatin","Fenoldopam","UTP","Cromoglicic acid","Betaine","(2R)-2-Hydroxy-3-(phosphonatooxy)propanoate","Hydroflumethiazide","Stearic acid","Sakuranetin","BICINE","Indapamide","Fluconazole","Atovaquone","6-Hydroxynicotinic acid","Chloramphenicol","Benzyl cinnamate","Zaleplon","Pipernonaline","Sulfanilamide","Ligustroside","N-Acetyl-L-aspartic acid","Acetaminophen glucuronide","Candoxatril","Atorvastatin","Mesobilirubinogen","Pirenzepine","2-benzylbutanedioic acid","9,10-Epoxyoctadecenoic acid","Practolol","Beta-Carboline","Canavanine","3-(4-Hydroxyphenyl)-1-(4-hydroxy-2-methoxyphenyl)-2-propen-1-one","Genistein","Limocitrin","Dimethylbenzimidazole","(9Z,12Z,15Z)-Octadecatrienoic acid","Vardenafil","Caffeate","3-(3,4-Dihydroxy-5-methoxy)-2-propenoic acid","Tiagabine","1-(2,6-Dihydroxy-4-methoxyphenyl)-3-phenyl-1-propanone","Thyrotropin releasing hormone","(+)-Sesamin","19(S)-HETE","LS-Tetrasaccharide b","2-linoleoyl-sn-glycero-3-phosphocholine","Phenylethyl primeveroside","7,8-Dihydroneopterin","EPA (d5)","Traumatic Acid","Prostaglandin J2","Indolelactate","4-Hydroxybenzyl alcohol","N-Acetylasparagine","1-Methyluric acid","Quinate","Prulaurasin","3,5-Diiodo-L-tyrosine","Maltol","Progesterone","Cytokinin B","Flecainide","Benzylamine","CTP","Isonicotinic acid","Taurine","D-Fructose","3-(4-Hydroxyphenyl)pyruvate","1-Naphthol","1-Naphthaleneacetic acid","Zalcitabine","Hydrocinnamic acid","Arachidic acid","Leukotriene F4","Dapsone","Probucol","Formylanthranilic acid","Ochratoxin A","Fluticasone propionate","O-Phosphotyrosine","Fructose 1,6-bisphosphate","L-Homoserine","9(S)-HPODE","1,11-Undecanedicarboxylic acid","Enalapril","L-Threonine","Nelfinavir","6-Thiourate","Eprosartan","5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-8-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-4H-chromen-4-one","3-Hydroxyvalproic acid","4-Aminophenol","(-)-Guttiferone E","Myristoleic acid","Pyridoxal","Isoliquiritigenin","(4-Hydroxybenzoyl)choline","Thiamine monophosphate","Podofilox","1-Aminocyclohexanecarboxylic acid","Acetohexamide","8-Hydroxyguanosine","Fenitrothion","alpha-Ketoisovaleric acid","Ganoderic acid G","Indan-1-ol","3-Hydroxy-carbofuran","1-palmitoylglycerophosphocholine","Glutamylglutamic acid","Pentostatin","Glabrone","Fucose 1-phosphate","Salicin","Rosmarinic acid","1-Methylguanosine","dTMP","2,4-Dichlorophenoxyacetic acid","4-Hydroxyproline","Cryptotanshinone","Celastrol","Ethyl glucuronide","Nevskin","D-Mannose","Alternariol","cis,cis-Muconate","3-Methoxytyramine","Austalide H","dTDP-D-glucose","Spironolactone","Demethylated antipyrine","L-Norleucine","Azlocillin","L-Tryptophan","Adouetine X","Pentadecanoic acid","Amygdalin","Penicillin V","Glutamylthreonine","Kaempferol","Dihydrolipoate","Phenylacetylglycine","Penciclovir","dCMP","Prolylhydroxyproline","Nifedipine","L-Arabinose","Epiandrosterone","2-Methoxyestradiol","PQQ","Flutamide","Benzyl isothiocyanate","Dimethylallylpyrophosphate","L-Valine","ATP","Melanin","Rhein","(3'alpha,5'alpha,9'xi,10'beta)-O-(3-Hydroxy-7-drimen-11-yl)umbelliferone","Quinapril","N-Acetylserotonin","4-Acetamidobutanoate","Nilutamide","Morphine","Diflunisal","Minoxidil","N2-gamma-Glutamylglutamine","16-Hydroxy hexadecanoic acid","Caprylic acid","Fluvastatin","2,4-Dichlorophenol","Azacitidine","D-2-Hydroxyglutaric acid","Nordiazepam","Aciclovir","alpha-Isopropylmalate","Cholesterol sulfate","Ferulate","Dihydrojasmonic acid","Emtricitabine","Steviobioside","L-Cystine","Gallic acid","N2,N2-Dimethylguanosine","Ergocalciferol","Guanidinosuccinic acid","3-Methylsalicylate","Coumarin","Quinine","Gibberellin A53","Arformoterol","L-Malic acid","Deferasirox","Cyanuric acid","Dehydroepiandrosterone","Carglumic acid","Myristic acid","Carvedilol","Brassinolide","(3S,5R,6R,7E)-3,5,6-Trihydroxy-7-megastigmen-9-one","Adipic acid","1-Deoxy-D-xylulose 5-phosphate","Gluconolactone","Phenacemide","3-Methylthiopropionic acid","Hippuric acid","Enterolactone","N-Acetylaspartylglutamate","3-Aminosalicylic acid","Alpha-Lactose","Phenylethylamine","5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1