MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/m_MTBLS15552_LC-MS_positive_hilic_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/m_MTBLS15552_LC-MS_negative_hilic_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/s_MTBLS15552.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/a_MTBLS15552_LC-MS_negative_hilic.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/a_MTBLS15552_LC-MS_positive_hilic.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/A3.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/B2.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/B3.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/A1.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/QC01.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/QC03.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/A2.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/A2.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/QC02.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/QC03.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/QC02.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/B3.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/B1.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/QC01.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/B1.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/A3.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/A1.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/B2.mzMLftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/mgf/TSTQK25635a_mix02_P.mgfftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/mgf/TSTQK25635a_mix02_N.mgfftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/NEG/mgf/TSTQK25635a_mix01_N.mgfftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552/FILES/DERIVED_FILES/POS/mgf/TSTQK25635a_mix01_P.mgfprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS15552<p>After correction and filtering, metabolite identification was performed by searching the peaks against the laboratory's in-house database, integrated public databases, and a prediction library. Ultimately, features with a comprehensive identification score&nbsp;0.5 and a QC sample CV &lt; 0.3 were retained. Data from positive and negative ion modes were then merged, retaining the feature with the highest identification confidence level and the smallest CV value, to generate the file 'all_sample_data.xlsx'.</p>MetaboLightsPublicLiquid Chromatography MS - positive - hilicLiquid Chromatography MS - negative - hilic<p>All samples were for two LC/MS methods. One aliquot was analyzed using positive ion conditions and was eluted from T3 column (Waters ACQUITY Premier HSS T3 Column 1.8 µm, 2.1 mm all_fetch_status all_status eb_eye_copy_status eb_eye_entry_counts eb_eye_fetch_status eb_eye_metabolights_complete.xml eb_eye_metabolights_compounds.copy eb_eye_metabolights_compounds.xml eb_eye_metabolights_studies.copy e_fetch_status europe_PMC_metabolights_studies.copy europe_PMC_metabolights_studies.xml head.xml studies.copy study.xml tail.xml thomsonreuters_metabolights_studies.copy thomsonreuters_metabolights_studies.xml 100 mm) using 0.1 % formic acid in water as solvent A and 0.1 % formic acid in acetonitrile as solvent B in the following gradient: 5 to 20 % in 1 min, increased to 99 % in the following 2 mins and held for 1.5 min,then come back to 5 % mobile phase B witnin 0.1 min, held for 1.4 min. The analytical conditions were as follows, column temperature, 40 °C; flow rate, 0.4 mL/min; injection volume, 3 μL; Another aliquot was using negative ion conditions and was the same as the elution gradient of positive mode.</p>M3-Driven Hexosamine Biosynthesis Facilitates Hepatocellular Carcinoma Progression through YBX1 O-GlcNAcylation.The First Affiliated Hospital of Anhui Medical UniversityJiaqing Chencellmass spectrometry assay<p>The sample stored at -80 °C refrigerator was thawed on ice. A 500 μL solution (Methanol : Water=4:1, V/V) containing internal standard was added into the cell sample and vortexed for 3 min. The sample was placed in liquid nitrogen for 5 min and on the dry ice for 5 min, and then thawed on ice and vortexed for 2 min. This freeze-thaw circle was repeated three times in total. The sample was centrifuged at 12000 rpm for 10 min (4 °C). A 300 μL of supernatant was collected and placed in -20 °C for 30 min.The sample was then centrifuged at 12000 rpm for 3 min (4 °C). A 200 μL aliquots of supernatant were transferred for LC-MS analysis.</p>Homo sapienshttps://www.ebi.ac.uk/metabolights/MTBLS15552Jiaqing Chen. The First Affiliated Hospital of Anhui Medical University. 2345011394@stu.ahmu.edu.cn.Beicheng Sun. The First Affiliated Hospital of Anhui Medical University. 2345011394@stu.ahmu.edu.cn.<p>Raw mass spectrometry data were converted to the **mzML** format using ProteoWizard. Peak detection, alignment, and retention time correction were then performed using 'XCMS'.</p>Group2345011394@stu.ahmu.edu.cn<p>PGM3-overexpressing and control cell samples (3 biological replicates per group, 1 × 1000000 cells per sample), then samples were flash-frozen in liquid nitrogen and stored at 80 °C prior to metabolomic analysis.</p>MetabolomicsMetabolomicsFR054untargeted analysisThermo Scientific Orbitrap Exploris 120Homo sapiensHepatocellular carcinomaYBX1cellThermo Scientific Vanquish UHPLC SystemHCC-Hep3B cellPGM3Hexosamine biosynthesis pathwayO-GlcNAcylationMetabolomicsFR054untargeted analysisThermo Scientific Orbitrap Exploris 120Homo sapiensHepatocellular carcinomaYBX1cellThermo Scientific Vanquish UHPLC SystemHCC-Hep3B cellPGM3Hexosamine biosynthesis pathwayO-GlcNAcylation<p>All the methods alternated between full scan MS and data dependent MSn scans using dynamic ex-clusion. MS analyses were carried out using electrospray ionization in the positive ion mode and negativeion mode using full scan analysis over m/z 70-1000 at 60000 resolution. Additional MS settings are: ionspray voltage, 3.8 KV or 3.4 KV in positive or negative modes, respevtively; Sheath gas (Arb), 60; Aux gas, 20; Ion transfer tube temperature, 320 °C; Vaporizer temperature, 350 °C; Collision energy, 30,40,50V; Top N vs Top speed, 10.</p>4,6-Dinitro-O-cresol9,10-DHOMEDiethyl hydrogen phosphateL-thyronineUridine-5'-diphosphatecis-3-Hexenyl pyruvatePyrocatechol3,3-Dimethylglutaric acidIsothiocyanatocyclohexanealphLinolenic acidFolic acid2-Acetamido-3-methylbutanoic acidLenthionine(4-Amino-2-methylpyrimidin-5-YL)methyl dihydrogen phosphateHeptanoic acidPI(18:0_20:4)2-Methylbenzoic acidDimethyl hydrogen phosphatePE-NMe2(20:3_16:0)gammLinolenic AcidTetracosanoic acidDehydroabietic acidGabazine8,11-Eicosadienoic acidPG(20:4_18:0)Citrulline3-Hydroxy-6,8-dimethoxy-7(11)-eremophilen-12,8-olideAlloxanTropoloneFlavin mononucleotidePhenol2-Ep5-epvaliolone 7-phosphateUridine-5'-monophosphatePS(22:6_22:4)1-Methyl-4-nitroimidazole2-Iminiopropanoate4-(Phosphooxymethyl)-2-furancarboxaldehyde3-Hydroxyanthranilic acidMethyl dihydrogen phosphate4-Hydroxybenzaldehyde2'-Phospho-5'-adenylyl sulfate5-Hydroxyindoleacetic acidPS(20:3_22:5)PE-NMe(18:0_15:0)LPC(15:0_0:0)Prostaglandin E2trans-10-Octadecenoic acid1-(1Z-octadecenyl)-sn-glycero-3-phosphocholinePE-NMe2(18:1_16:0)GlycineMethanesulfonic AcidLPA(20:2_0:0)Glutaric acid2-Hydroxyquinoline9E-heptadecenoic acid1-Methyl-3-(2-methyl-1-propenyl)cyclopentane2-Amino-4,6-dichloropyrimidine-5-carbaldehydeLPE(0:0_18:2)5,6-Indolequinone-2-carboxylic acid4-MethylcatecholGlutathionethromboxane B2Panaxytriol[(2R)-2-(hexadecanoyloxy)-3-hydroxypropoxy]phosphonic acidN-PhenylacetylglycineMiglitolDimethyl tetrasulfide1-16:0-2-18:2-Phosphatidylinositol12alphHydroxy-3-oxochol4,6-dien-24-oic AcidN-AcetylvanilalaninePseudouridineMonoethyl carbonatePA(18:0_22:5)4-(1,1,3,3-Tetramethylbutyl)-phenol3-Oxoadipic acidOleamide2-Ethyl-2-Hydroxybutyric acidPS(16:0_22:0)5,15-DiHETEPantothenic acidN-NitrosoguvacolineCitral propylene glycol acetalAmyl Nitrite3-[(2-Hydroxy-3,3-dimethyl-4-phosphonooxybutanoyl)amino]propanoic acidPE-NMe2(18:1_14:0)Isovaleric acidGuanosineGlyceraldehyde2'-Deoxyguanosine-5'-diphosphatePE-NMe2(16:1_20:4)3-Hydroxydecanoic acid1,2,3,4-Tetrahydronaphthalene7-Ketocholesterol1,3-Cyclohexanedione5-Hydroxyferulic acidPE-NMe2(18:2_18:1)5-Chloro-3-(4-methylsulfonylphenyl)-2-pyridin-3-ylpyridineIndoleacetaldehydePhoximOleoyltaurineSuccinyladenosinedTDP-4-keto-5-methyl-betL-rhamnose3-MethylxanthineAcetylglycineAcetoacetic acidGlyceric acid1,2-Dipalmitoleoyl-sn-glycero-3-phosphocholinePA(18:4_18:4)(2R)-2-[[(2S,3R)-3-amino-2-hydroxy-4-phenyl-butanoyl]amino]-4-methyl-pentanoic acidPhthalic acid1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphoethanolamineValeraldehyde dibutyl acetalMaleimidePE-NMe(16:1_15:0)2-Aminoisobutyric acidPE-NMe2(16:1_20:3)L-3-Cyanoalanine3-tert-Butyl-4-hydroxyanisoleProstaglandin D32-Phosphoglyceric acidDaidzein 4'-O-glucuronideN-Nitrosoguvacinetrans-trans-Muconic acid1-Hexadecanoyl-sn-glycero-3-phospho-(1'-myo-inositol)PyrophosphateRhamnoseUridine3-Ethylphenyl sulfate4-Amino-2-methylenebutanoic acid3'-Adenylic acid1,3-BenzenediolLyxo-2-HexuloseTulipalin BGlu-PheOrnithine2-PentadecanoneN-Palmitoyl TaurineN-Acetylaspartylglutamic acid10-Undecenal3-Hydroxybenzoic acid4-HydroxyphenylacetaldehydeCysteineNitroethaneSerineSterculic acid2,4-Diamino-6-nitrotolueneProlineBenzoyl phosphate12-Methyltetradecanoic acidIsopentenyladenine5'-Deoxy-5'-methylthioadenosineMonomethyl fumarate2,5-Dichloro-1,4-benzoquinone1-Naphthoic acidGlu-Met3-Hydroxymethylglutaric acidPE-NMe(15:0_18:0)Aspartic acidTagatoseN,N'-DiacetylhydrazineHydroxyisoleucine2,4,6-Triethyl-1,3,5-trioxaneIsoniazid1,2-DichloroethaneAcetimidoquinonePiperonalAdenosineAdenosine monophosphate2-Hydroxy-3-(sulfooxy)benzoic acidMonoethyl phthalatePE-NMe2(18:1_14:1)AllopurinolPE-NMe(18:1_18:1)Ethylene carbonateHMG-CoA3-Methylpyrrolo[1,2-a]pyrazineHeptadecanalPS(18:1_24:1)1-Palmitoylglycerol 3-phosphateFFA(16:1)2-Hydroxycinnamic acid12,13-DiHOME(Z)-2-hydroxy-3-aminoperacrylic acid2,3-Dihydroxy-2'-carboxybiphenyl3-(4-oxo-4,5-dihydro-1H-imidazol-5-yl)propanoic acidPS(22:4_22:5)1,2-Epoxyhexadecane5-Phenylvaleric acid10-hydroxystearic acidNeoabietic acidBerteroinEthylnitronate1,6-HexanedithiolAspartate semialdehydeBenzoic acid2-amino-3-(1H-pyrazol-1-yl)propanoic acidAscorbic acid5-Methylcytosine(R)-DihydromaleimideD-QuinovoseChinomethionat2-Azaniumyl-5-(carbamoylamino)pentanoateTraumatic acidIsoproterenolDocosahexaenoic acidD-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate1-(1Z-octadecenyl)-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine1,2-Dipalmitoyl-sn-glycero-3-phosphoethanolamineThymidine-5'-phosphate1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine-N,N-dimethylUridine diphosphate glucose15-methyl palmitic acid2,5-DihydroxybenzaldehydePyrazin-2-carboxylic acidPropylene glycol diacetate(S)-10,16-Dihydroxyhexadecanoic acidPE-NMe2(16:1_16:1)PE-NMe2(18:0_14:0)Folinic acid2-Dodecylbenzenesulfonic acidThreonineMethyl ( )-2-methylpentanoate(3S,3aS,6R,8aS)-3,8-Dimethyl-5-(propan-2-ylidene)-2,3,4,5,6,8hexahydro-1H-3a,6-epoxyazulen-6-olAcetylsalvipisone2-Ketobutyric acid(3beta)-Stigmast-5-en-3-yl 6-O-palmitoyl-betD-glucopyranosideUrocanic acidValeric acidOleic estolideDinexAcetaminophenLysineLombricineLPC(14:0_0:0)4,4'-DihydroxybenzophenoneSclareolideHydroxyoctanoic acidLPE(0:0_16:1)Pyruvatoxime1-Oleoyl-2-myristoyl-sn-glycero-3-phosphocholineLPC(18:0_0:0)Glutamic acid1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoethanolamine4-NitroanilineMethoxypyrazine2,4-Dichlorobenzoic acidSuberic acidPE-NMe2(15:0_15:0)Acetylsalicylic acid2-O-Methylcytosine3-(Hydroxymethyl)-2-octanoneGuaninePiribedil2-Naphthol4-NitrophenolButylparaben1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamineAdenosine 5'-DiphosphateDimethyl sulfoneLPE(0:0_16:0)2-(1-methyl-1H-imidazol-5-yl)acetic acidPE-NMe2(18:2_24:0)CreatinineNitrobenzeneSpinoside APetroselinic acidDidox3-methoxybenzene-1,2-diolGlu-ValXanthosine(S)-3,7-Dimethyl-1,6-octadienePyridoxinePimelic acidcis-7-Hexadecenoic acid1-Tetradecanoyl-2-eicosanoyl-glycero-3-phosphoserineCitric acid3-Aminopentanedioic acidOxamic acid3-Hydroxy-3-methyloxindoleValineGlycolithocholic acidHydroxymethylphosphonateN-Acetylleucine(S)-2-amino-6-oxopimelic acidMaleamic acidProcarbazineOleic AcidPE-NMe(15:0_20:3)PC(16:0_P-18:0)Ethyl nitrite5,8,11-Eicosatrienoic acidMethylparabenPipecolic acidMultifidolFenoldopamSodium malateMethyl 4-chloro-1H-indole-3-acetate5-Fluorouridine4-Hydroxyphenyl thiocyanate2-Methyl-3-heptanoneN-Acetylimidazole(5R)-5-methoxypyrrolidin-2-oneBetaineLPE(0:0_18:0)N-Methylhydantoin10-formyldihydrofolic acidIndole-3-carboxaldehydeGlu-TyrFlavin adenine dinucleotideOrotidineJasmonic acid2-(1H-Imidazol-1-Yl)Acetic Acid3-Phenyllactic acid24,25-Diacetylvulgaroside5,6-dihydrothyminegammGlutamylglutamate1,1-Dichloroethane4-HydroxyphenylglycineSalicylhydroxamic acidHydroquinoneSodium cyclamateN-Acetyl-L-aspartic acidLobelineBenzofuran1-(4-Hydroxy-3-methoxyphenyl)-3-decanone2-Amino-4-nitrophenol2-MethylbutyronitrileO-acetyl-L-serineMonobutyl phthalate(S)-2-Hydroxy-2-phenylacetonitrile O-[b-D-apiosyl-(1->2)-b-D-glucoside]ChloroxylenolDimorphecolic acid1,1-Dimethoxyheptane2-Methylheptanoic acidPE-NMe2(24:0_22:0)12-Oxo-2,3-dinor-10,15-phytodienoic acid3-Hydroxyisovaleric acid1-(9Z-hexadecenoyl)-2-hexadecanoyl-glycero-3-phosphocholineDodecanoic acidGlyoxylic acidSphingomyelins10-Hydroxydecanoic acid2-CyanopyrimidineParaquat dichloride(+_-)-Ethyl 2-hydroxy-2-methylbutyrateIsopimaric acidPC(18:0_18:2)2-Methyl-5,7-dihydrothieno[3,4-d]pyrimidine4-Methylvaleric AcidXylonic acid5-Methylhexanoic acid5-Oxo-4,5-dihydro-2-furylacetic acidN-MethylalaninePhosphatidylserine4-CarboxypyrazoleAdenosine-5'-triphosphate13,16,19-Docosatrienoic acidThyminePG(18:0_18:1)Methyl 10-gingerolPS(22:4_20:3)2-Carboxy-5,7-dimethyl-4-octanolide2-AcetylaminofluorenePS(20:0_18:0)Pelargonic acidTxB3Pyrogallol-1-O-sulphateMesalazineN-(2,3-dihydroxybenzoyl)-L-serineSarcosineSulfateLactic acid6,7-BenzocoumarinDichlorpropIsonicotinic acidTaurine2,5-DihydroxypyridineEpothilone DFurfuryl acetateIle-Asp3,3'-Dithiobis[2-methylfuran]Licochalcone BMethyl 1-(1-propenylsulfinyl)propyl disulfide2-Aminonicotinic acid7-Chloro-2-dibenzofuranol2-Methylvaleric acid2-HydroxybenzaldehydeFormylanthranilic acidcytidine monophosphate N-acetylneuraminic acidPS(22:5_22:5)1,11-Undecanedicarboxylic acid2-Formylglutaric acid4-Guanidinobutyric acid5-Hydroxyvalproic acidIminoacetic acid8-Amino-7-oxononanoic acidN-Formylmethionine2-(2-Thienyl)furan3-Hydroxyvalproic acidPE-NMe2(16:1_14:0)Pentitol3-Indoleacrylic acidcyclic ADP-ribose4-Amino-3-hydroxypyridine2,3-Dihydro-2-methylthiophenePE-NMe(18:1_15:0)Benzenesulfonic acid, undecyl-2-Methyl-4-(pyridin-3-ylethynyl)thiazoleDocusateYuzu-LactoneMethionineN-Acetyl-D-glucosamine3-Hydroxynonyl acetateDiacereinPS(20:1_20:1)trans-Vaccenic acid2,5-DiethyltetrahydrofuranForskolinNicotinamide Adenine Dinucleotide Phosphate2-Amino-3-oxoadipateGuanosine-5'-monophosphatecis-11-Eicosenoic acid3-Hydroxydodecanoic acidSuccinimide4-Hydroxyproline6-ketoprostaglandin E14-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol1,5-Dioxaspiro[5.5]undecan-3-ol, 10-methyl-7-(1-methylethyl)-1,1-Dimethyl-3-phenylpropyl acetateDimethoxanePyrrole-2-carboxylic acid4-Nitro-o-phenylenediamine1,1-Dimethoxynonanecis,cis-Muconic acidL-NorleucineOctopamine4-Methyl-2-pentyl-1,3-dioxolane3-(N-Nitrosomethylamino)propionitrile4-[(E)-2-(1,2-dicarboxyethylamino)vinyl]-2,3-dihydropyridine-2,6-dicarboxylic acid4-HydroxymethylpyrazolePE-NMe2(20:4_16:0)PG(22:6_18:0)Pentadecanoic acidAzacridone AN,N-dihydroxy-L-tryptophanateGlu-gluGlycocyamineDopamine4-Hydroxycrotonic acid1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholineGlycidyl stearatep-CoumaraldehydeKojic acidL-HomoarginineHC Blue 1Gentiatibetine8,15-Dihete(Z)-3-aminoacrylic acidEicosadienoic acidphosphoribosyl-AMP2-Chloro-(1,1'-biphenyl)-4,4'-diolPE-NMe2(20:4_16:1)2-Hydroxyhexadecanoic acidPS(20:4_22:5)HydroxychlorEicosapentaenoic acidUracilN-oleoylglycines-Hexylglutathione2-Hydroxyacetophenone1,7-Dimethyluric acid2,4-Hexadienoic acid8,9-Epoxyeicosatrienoic acid1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine3-Methylbenzaldehyde2-Ammonio-3-{[(2-ammonioethoxy)phosphinato]oxy}propanoate4-Oxo-L-prolineCreatineCosmosiinInosinic acid4-[2-Hydroxy-3-(propan-2-ylamino)propoxy]-3-prop-2-enylphenol5-Aminolevulinic acido-Methoxyphenyl sulfateOleoylcarnitine9-Oxo-nonanoic acidOxiglutationePE-NMe2(24:0_24:0)Behenic acidCholesterol sulfateCytosinePE(18:0_20:4)1,2-benzisothiazol-3(2H)-oneDihydrojasmonic acid5-betD-Ribofuranosylpicolinamide adenine-dinucleotideIsopentenyl pyrophosphateEthylmethylacetic acid2-[(2E)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-1,4-dihydronaphthalene-1,4-dione4-Ethylphenyl sulfate9,10-Dihydroxystearic acidPurpurinGrevillolLPE(18:1_0:0)3-Oxooctadecanoic acid3-Amino-3-(4-hydroxyphenyl)propanoic acid12-Methyltridecanoic acidGlyceraldehyde-3-phosphatePyrocatechol sulfateHydroxyquinoline1,2,3,5,6,8-HexathionaneHymexazolPC(18:1_15:0)Myristic acidArabitolAcetohydroxamic AcidParaxanthineL-Cysteine, S-propyl-HypoxanthinetyrosinePE-NMe2(24:0_24:1)Acetic acid2,4-DinitrophenolPsilocybineDephospho-CoAAdrenic acidPE-NMe2(16:1_16:0)1,2-Dioleoyl-sn-Glycero-3-Phosphocholine4-Dodecylbenzenesulfonic acidDinoterbPermethrinHippuric acidEthofumesate2,4,6-Trihydroxybenzoic acidFuberidazoleFlavidulol A4-Hydroxy-9-fluorenone2-Methylhexano-6-lactoneArabinose3-Aminopiperidine-2,6-dioneMethocarbamolGDP-L-fucoseN-acetylmuramic acid 1-phosphate2-Hydroxy-4-imino-2,5-cyclohexadienoneUDP-beta-L-threo-pentopyranos-4-ulose2-Hydroxy-3-(phosphonooxy)propyl stearateOxaloglutarate1,2-Dioleoyl-sn-glycero-3-phosphateUndecylenic acid4-Formyl-2-hydroxybenzoic acid2-Methyl-3-hydroxybutyric acidVernolic acid3-Hydroxy-5Z-octenyl acetatecoenzyme F420-1phenylalanineBenzene oxide5alphAndrostane5-oxoETE3-hydroxy-tetradecanoic acidLythramineOxoadipic acidL-PropargylglycinePS(22:5_22:4)Isobutyric acidprostaglandin B22-Hydroxy-3-(1H-imidazol-5-yl)propanoic acid1-Vaccenoyl-2-pentadecanoyl-sn-glycero-3-phosphocholine12-HOMEAceglutamide4-Hydroxy-3-methylbenzaldehyde2-Ethylhexanoic acid1,2-DihydroaceanthryleneRibose-1-phosphateUridine-5'-diphospho-N-acetylgalactosamine disodium saltIsoxazolin-5-one1,3-Dihydroimidazol-2-oneInosinePurineNonanal propyleneglycol acetal2-Methylsuccinic AcidArabinosylhypoxanthineLPE(18:0_0:0)LumichromeHexane, 1,1'-[ethylidenebis(oxy)]bis-GlutamineTerpendole ELevonordefrinPhenylacetic acidPA(20:1_22:6)2,2-Dimethylbutyric acidCholic acid3,4-Dimethylbenzoic acidPalmitic acidArachidonic acidFirefly luciferinEthenyl acetateHistidine16-Hydroxyhexadecanoic acid1-Stearoyl-2-linoleoyl-sn-glycero-3-phosphoethanolamineImidazole-4-methanolPA(20:0_18:3)Valylcysteine2-Aminoacrylic acidEpoxyeremopetasinorolTyramine1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholineQuinaldine3-HydroxybenzaldehydeBenzenebutanoic acidNervonic acidDexrazoxane4-CDP-2-C-methyl-D-erythritolMoschamine(S)-Methylmalonic acid semialdehyde(S)-14-Methylhexadecanoic acidDodecanal dimethyl acetalSebacic acidPhosphoric Acid2-Hydroxystearic acidPE-NMe2(18:0_18:4)N-hydroxy-L-isoleucine3-Hexenedioic acidDicambaResolvin D1NorfenefrinePhenol red2-Methyl-2-(methyldithio)propanal1,2-Dipalmitoleoyl-sn-glycero-3-phosphoethanolamineBovinic acidOrotidylic acid2,4,4-TrimethylcyclopentanonePE(P-18:0_22:6)L-Menthyl (R,S)-3-hydroxybutyrateEthyl isopropyl ketoneAcetylenedicarboxylic acidTax4(20),11(12)-dien-5alphyl acetateDihydrocaffeoyl-CoAPicolinic acid7,9-DocosanedioneSuccinic acid semialdehyde2-AminobenzimidazoleFurfuryl alcoholAstragalin4-Hydroxy-3-methylbenzoic acidPyroglutamic acid3-Hydroxyoctanoic acidCoenzyme AS-Glutathionyl-L-cysteineCyclocreatinetrans-Zeatin riboside triphosphateIsopalmitic acidHydroxyphenyllactic acidAlanineLevulinic acidDodecanedioic acidTryptophanLinoelaidic acidXanthine4-Imidazoloneh-gammGlu-leu-oh3-Hydroxyhexadecanoic acidADP-riboseDL-DopaPrednisone acetateUridine diphosphate glucuronic acidN-Acetyl-betalaninePE-NMe2(18:1_18:1)Heptyl ketone1-arachidonoyl-sn-glycero-3-phospho-1D-myo-inositol1-Stearoylglycerophosphoserine2-Hydroxybutanoic AcidN-Acetyl-L-alanineLPS(22:6)Caryoptin(x)-2-Heptanol glucosideDeoxy-5-methylcytosine-esterPhenyl acetate2-amino-5-formylamino-6-(5-phosphoribosylamino)pyrimidin-4(3H)-oneNicotinic acid1-(11Z-octadecenoyl)-2-hexadecanoyl-sn-glycero-3-phosphocholine5-HydroxymethyluracilNorsalsolinol1,3,5-Trichloro-2-methoxybenzene5-Acetylamino-6-formylamino-3-methyluracil2,6-Diamino-4-nitrotolueneFFA(19:1)PantetheineTiglylglycineIndole-3-acetamide2-(((2-Ethylhexyl)oxy)carbonyl)benzoic acidButyl nitriteFurmecyclox2-hydroxyacrylic Acid4-Amino-3-hydroxybutyrate4-Methyl-2-(1-phenylethyl)-1,3-dioxolane, 9CIMalic acidNicotinamide N-oxide3-Oxododecanoic acid3-Phosphoglyceric acid1-Methyl-3-(2-methyl-2-propenyl)-cyclopentane2-PiperidinoneHydriodic acidDaphnetin7-MethylxanthineIsobutyrylglycineo-Tyrosine16-Oxohexadecanoic acidDimethyl carbonate1-octadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoserine4-Hydroxybenzenesulfonic acidPE-NMe2(18:1_16:1)N-Methyl-aminoisobutyric acidPE-NMe2(18:2_16:0)3-MethylindoleUndecanedioic acid1-Oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine2-Hydroxy-2-methylbutyric acidTraumatin2-Isopropyl-4-methyl-1,3-dioxolaneOxypurinolPyruvic Acid4'-PhosphopantetheineSedoheptulose12-Hydroxystearic acidEpigallocatechinPA(22:6_22:2)Deoxycytidine diphosphateGuanosine-5'-diphosphateHydantoin5-amino-1H-imidazole-4-carboxylic acidElaidic acidLPI(18:1)(S)-Mandelic acid O-betD-GlucopyranosidePE-NMe2(18:2_16:1)p-CresolVaporoleAzelaic acid(S)-2-hydroxy-3-(1H-imidazol-4-yl)propanoic acid9,10-Epoxystearic acidPC(18:1_P-16:0)(E)-but-2-enedioate;hydronValproic AcidPerillic acid1-O-Hexadecyl-lyso-sn-glycero-3-phosphocholineEpinephrineAnigorufoneLacto-N-triaoseBenzoyl chlorideKurarinol4-Chloro-L-phenylalanineChlormephosCytidine-5'-diphosphate(Z)-5-[(5-Methyl-2-thienyl)methylene]-2(5H)-furanoneImidazoleacetic acidHexadecenoic acid2-Methoxy-6-methylpyrazineGlycolaldehydeTartaric acidDemanyl phosphate9-beta-d-ArabinofuranosylguanineFAA(18:1)3b-Hydroxy-5-cholenoic acidErythrulose1-Heptadecanoyl-sn-glycero-3-phosphocholineNorvalineVanillinMethylmalonic Acid1-octadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphoethanolamineSinapoylspermine5-(1,1-Dimethylheptyl)-2-[5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]phenolfalseM3-Driven Hexosamine Biosynthesis Facilitates Hepatocellular Carcinoma Progression through YBX1 O-GlcNAcylationPhosphoglucomutase 3 (PGM3) is one of the rate-limiting enzymes in the hexosamine biosynthesis pathway (HBP) and a key regulator of HBP metabolic flux. Despite the functional role of PGM3 has been validated in various tumors, its function and molecular mechanism in hepatocellular carcinoma (HCC) remain to be elucidated. This study found that PGM3 expression is upregulated in HCC tissues, and high PGM3 expression is closely associated with poor prognosis in HCC patients. In vitro and in vivo results demonstrated that PGM3 enhances UDP-GlcNAc synthesis and protein O-GlcNAcylation, thereby promoting HCC proliferation, migration, and invasion. Further O-GlcNAcylomic sequencing of HCC cells identified Y-box binding protein 1 (YBX1) as a key substrate for PGM3-mediated O-GlcNAcylation. Notably, O-GlcNAcylation of YBX1 at a specific serine residue (Ser165) enhances its nuclear translocation. Additionally, we validated that FR054, a novel reported PGM3 inhibitor, retards HCC progression by diminishing PGM3-mediated O-GlcNAcylation. These interventions effectively inhibit HCC malignant progression. Collectively, our findings reveal the potential therapeutic value of targeting the PGM3-HBP-YBX1 signaling axis in HCC 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