{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_HepG2_intracellular_Intactglycopeptide_TMT_Run3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_HepG2_intracellular_Intactglycopeptide_TMT_Run2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_SMMC-7721_intracellular_Proteomics_TMT.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_SMMC-7721_intracellular_Intactglycopeptide_TMT_Run2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_SMMC-7721_intracellular_Intactglycopeptide_TMT_Run1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_HepG2_intracellular_Proteomics_TMT_Run1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_HepG2_intracellular_Proteomics_TMT_Run2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/JiaLi_HepG2_intracellular_Intactglycopeptide_TMT_Run1.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD017033/Excel_results.rar"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["lijia_glyco@163.com"],"submitter":["Li Jia"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"disease":["Hepatocellular Carcinoma"],"software":["Not available"],"submitter_keywords":["Glycoproteome","Site-specific glycosylation","Hepatocellular carcinoma","Intact glycopeptide","Emt","Mass spectrometry"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD017033"],"tissue":["Epithelial Cell","Cell Culture"],"sample_protocol":["Human hepatocellular carcinoma cell lines SMMC-7721 and HepG2 were cultured in DMEM medium supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a humid atmosphere of 5% CO2 for the first three generations. Then the medium was changed to the basic medium (without FBS) for the next eight hours before adding 10 ng/ml HGF. Cellular proteins were then harvested at six different time pointswithin 72 hours (0, 6, 12, 24, 48 and 72 h).The cellular proteins were denatured in 8 M urea/1 M NH4HCO3 buffer,and reduced by 5 mM dithiothreitol (DTT) at 37 °C for 1 h and alkylated by 15 mM iodoacetamide (IAM) at room temperature in the dark for 30 mins. Another 2.5 mM DTT was then added and incubated at room temperature for 10 mins. The solutions were diluted two times with deionized water prior to the first cycle of protein digestion by incubating the samples with the sequencing grade trypsin (Promega, USA, WI; proteins: enzyme, 100:1, w/w) at 37 °C for 2 h with shaking. The solutions were further diluted four-fold with deionized water and the same relative amount of trypsin (proteins: enzyme, 100:1, w/w) was then added and incubated at 37 °C overnight with shaking. The pH of the solution was adjusted with 10% TFA till pH < 2. The samples were centrifuged at 15,000 g for 10 mins to remove any particulate matter and the peptides in supernatants were desalted by the HLB columns (Waters, USA). Peptides were eluted from HLB column in 60% ACN/0.1% TFA solution. The peptide concentrations were measured by BCA reagent. The tryptic peptides from different time points of HGF-treated cells were dried and re-dissolved in 50 mM HEPES solution (pH 8.5). The same amount of peptides from different time points were labeled by two sets of 10-plex Tandem Mass Tag (TMT) (Thermo Fisher, USA) reagents according to the manufacturer’s protocols. Set #1 and Set #2 were cellular proteins from SMMC-7721 and HepG2 cell lines. TMT reagents at 126, 127N, 127C, 128N, 128C, 129N labeled 0 h, 6 h, 12 h, 24 h, 48 h, and 72 h HGF-treated samples, respectively. The labeled samples within each TMT set were then pooled and desalted by HLB columns.The intact glycopeptides were enriched from TMT labeled samples using an anion exchange reversed phase (MAX) column . Briefly, the TMT labeled peptides eluted from HLB column were diluted by 100% ACN and TFA to the final concentration of 95% ACN/1% TFA. The MAX column (Waters, USA) were washed three times each by 100% ACN, 100 mM triethylammonium acetate buffer, deionized water, and 95% ACN/1% TFA, followed by sample loading twice and washes four times with 95% ACN/ 1% TFA. The glycopeptides bounding to the column were eluted in 400 μL of 50% ACN / 0.1% FA. The sample was dried by SpeedVac and resuspended in 20 μL of 0.1% FA."],"repository":["Pride"],"quantification_method":["TMT"],"modification":["TMT6plex-126 reporter+balance reagent acylated residue"],"data_protocol":["The peptides and enriched glycopeptides were analyzed by Orbitrap Fusion Lumos Mass Spectrometer (Thermo Scientific, Germany). The peptides were first separated on EASY-nLC™ 1200 instrument (Thermo Scientific, Germany) with a 75μm50cm acclaim PepMap separating C18 column (Thermo Scientific, Germany). For global peptide data, the MS/MS spectra were searched against reviewed human protein database downloaded from Uniprot website (www.uniprot.org/) at May 15, 2017, by Thermo Proteome Discover 2.2 (PD, Thermo Fisher Scientific, Germany). The search parameters were set as follows: up to two missed cleavage sites permitted for trypsin digestion, 10 ppm precursor mass tolerance, 0.06 Da fragment mass tolerance, carbamidomethylation (C, +57.0215 Da) as a fixed modification, and oxidization (M, +15.9949 Da) and deamidation (N, +0.98 Da) as dynamic modifications. The results were filtered with 1% FDR and at least two peptide-spectrum matches (PSMs) were required for a peptide. TMT labeling was used to quantify the peptides identified from LC-MS/MS data.The intact N-glycopeptide MS data were first converted to ‘mzML’ format using Trans-Proteome Pipline (TPP) and searched by an in-house software. The search parameters were set as follows: at least two oxonium ions out of the top 10 fragment ions in the MS/MS spectra were used for extraction of intact glycopeptide MS/MS spectra. The mass tolerances of 10 ppm and 20 ppm were allowed for precursor ions and fragmentation ions. The false discovery rate of identified intact glycopeptides was estimated by the decoy peptide method and 1% FDR was used as the identification cutoff. The identified intact glycopeptides were further filtered by ≥4 matched b/y ions of the peptide portion in the MS/MS spectra. The quantification information of glycopeptides were extracted from their identified MS/MS spectra based on intensities of their TMT reporter ions. The medium ratios of given glycopeptides were used as quantitation result, and the ratios between samples were further normalized by the normalization factors obtained from the global proteomic results."],"omics_type":["Proteomics"],"labhead":["Li Jia"],"instrument_platform":["Orbitrap Fusion Lumos"],"labhead_affiliation":["Northwest University"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["34093861 Jia L, Li J, Li P, Liu D, Li J, Shen J, Zhu B, Ma C, Zhao T, Lan R, Dang L, Li W, Sun S. Site-specific glycoproteomic analysis revealing increased core-fucosylation on FOLR1 enhances folate uptake capacity of HCC cells to promote EMT. Theranostics. 2021 11(14):6905-6921 10.7150/thno.56882"],"submitter_mail":["lijia_glyco@163.com"],"curator_keywords":["Biomedical"],"submitter_affiliation":["Northwest University"],"submitter_country":["China"],"pubmed_abstract":["Rationale: Epithelial-mesenchymal transition (EMT) has been recognized as an important step toward high invasion and metastasis of many cancers including hepatocellular carcinoma (HCC), while the mechanism for EMT promotion is still ambiguous. Methods: The dynamic alterations of site-specific glycosylation during HGF/TGF-β1-induced EMT process of three HCC cell lines were systematically investigated using precision glycoproteomic methods. The possible roles of EMT-related glycoproteins and site-specific glycans were further confirmed by various molecular biological approaches. Results: Using mass spectrometry-based glycoproteomic methods, we totally identified 2306 unique intact glycopeptides from SMMC-7721 and HepG2 cell lines, and found that core-fucosylated glycans were accounted for the largest proportion of complex N-glycans. Through quantification analysis of intact glycopeptides, we found that the majority of core-fucosylated intact glycopeptides from folate receptor α (FOLR1) were up-regulated in the three HGF-treated cell lines. Similarly, core-fucosylation of FOLR1 were up-regulated in SMMC-7721 and Hep3B cells with TGF-β1 treatment. Using molecular approaches, we further demonstrated that FUT8 was a driver for HGF/TGF-β1-induced EMT. The silencing of FUT8 reduced core-fucosylation and partially blocked the progress of HGF-induced EMT. Finally, we confirmed that the level of core-fucosylation on FOLR1 especially at the glycosite Asn-201 positively regulated the cellular uptake capacity of folates, and enhanced uptake of folates could promote the EMT of HCC cells. Conclusions: Based on the results, we proposed a potential pathway for HGF or TGF-β1-induced EMT of HCC cells: HGF or TGF-β1 treatment of HCC cells can increase the expression of glycosyltransferase FUT8 to up-regulate the core-fucosylation of N-glycans on glycoproteins including the FOLR1; core-fucosylation on FOLR1 can then enhance the folate uptake capacity to finally promote the EMT progress of HCC cells."],"pubmed_title":["Site-specific glycoproteomic analysis revealing increased core-fucosylation on FOLR1 enhances folate uptake capacity of HCC cells to promote EMT."],"pubmed_authors":["Jia Li L, Li Jun J, Li Pengfei P, Liu Didi D, Li Jing J, Shen Jiechen J, Zhu Bojing B, Ma Chen C, Zhao Ting T, Lan Rongxia R, Dang Liuyi L, Li Wang W, Sun Shisheng S"],"sample_synonyms":["HCC cell, dmMOF, Ass-1, HepG2 cell, TFA, fond, Particle, Hepatopoietin A, Basodexan, CycEI, Apaf-1, Long Term, Bca, 5730420M11Rik, DmelCG9648, Polypeptides, C230052L06Rik, dMOF, Line, Urea, 1, fold, 2, AGM4, WMS, O-2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl-(1-2)-O-5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl-(1-4)-N, (R*, bca, SET, C79325, SF|HGF, hac-1, N'-bis(aminoiminomethyl)-, SMMC-7721, weight-weight percentage, phosphatase 2A inhibitor I2PP2A, Salt, proteins, DmelCG4299, set, Strepto-Hefa, decreased, column, ACN, Acn, sample, Ambient, hepatocarcinoma cell, SGS, Degradations, ACETATE ION, anon-53Fa, Longterm Effect, l(2)SH0173, Ultrafine Fibers, Penicillin, HSF, Cyc E, ACMICD, bHLHd7, bHLHd6, BSF2, bHLHd9, bHLHd8, bHLHd5, bHLHd4, BG:DS07108.3, Streptomycine Panpharma, Bickel-Fanconi glycogenosis, l(2)05206, Ethanoat, CG6829, Estreptomicina Normon, Hydrogen Oxide, dark/hac-1/dapaf-1, glycogenosis due to GLUT2 deficiency, glycogen storage disease due to GLUT2 deficiency, Fiber, HLA-DR-associated protein II, DI-2, LY57, glycogenosis Fanconi EXACT, I-2Dm, Protein Digestions, pooled, reagent, hepatic carcinoma cell, scatter factor, inhibitor of granzyme A-activated DNase, c-Met, beta Trypsin, human, anions, HGF/SF, w/w, Scatter Factor, I-2PP1, Atmospheres, sample., liver adenocarcinoma cell, TAF-IBETA, TAF-Ibeta, SF/HGF, GSD type XI, Particulate Matter, TMT, Cleland Reagent, cycline, Effects, DmcyclinE, Streptomycin Grünenthal, 4-dimercapto-, Strepto Fatol, Carbamide, Ultrafine Particles, R*)-, cdi7, period, DmelCG3025, cyclinE, Azetat, Ly57, Gene Products, Cdi7, CDI7, anion, Growth Factor, Fanconi Bickel syndrome, Carmol, MAX, Acinus, Longterm, Ambient Particulate Matter, hepatic glycogenosis with Fanconi nephropathy, acetate, beta-Trypsin, Monosodium Salt, HPTA, 2pp2a, Long-Term, DmcycE, man, CG10574, Solution, Ultrafine, Lymphokines and Cytokines, acinusL, max, 2PP2A, acinusS, dSET, dSet, peptidos, Antibiotics, Hep-G2, 4-(2-hydroxyethyl)-, Particulate, GINGF, dark/dapaf-1/hac-1, mass percentage, Hep G2, Fanconi-Bickel disease, dApaf-1, Proteins, CG3025, Clelands Reagent, ion(1-), Factor, backward, buffer, Digestions, mKIAA0670, Cell, CD142, polypeptide, APAF1, l(2)k02514, Temperatures, DmCycE, Proteolyses, GGF1, carbonyldiamide, Hac-1, I-2PP2A, Long Term Effects, Dm I-2, HGF|SF, hepatic cancer cell, MFS1, glycogenosis, Cleland's, covalent modifier, l(2)k02602, underdeveloped, Dark/Dapaf-1/HAC1, HGFB, Longterm Effects, Cleland's Reagent, Gene Proteins, D-CycE, hepatorenal glycogenosis with renal fanconi syndrome, Isolation of Nuclei TAgged in specific Cell Types, Airborne, MeCO2 anion, reversed, Hac-1/Dark, IPP2A2, Fanconi syndrome with intestinal malabsorption and galactose intolerance, DmelCG6829, ethanoate, NK2, Hepatocyte, NK1, HEPES Monosodium Salt, peptide, Streptomycin Sulfate, Ccne, peptido, ClvPrd, BANF, HGFR, AA408052, IL-6, SMMC-7721 细胞, Apaf1, GSD due to GLUT2 deficiency, Effect, present in fewer numbers in organism, ARK, Penicillin Antibiotics, F-TCF, HEPES Monosodium, aniones, peptides, dermoid cyst with malignant transformation, Airborne Particulate Matter, TAF-I, E927b, dMax, 2610036I19Rik, 2610510L13Rik, hypoplasia, SF, arc, Air Pollutants, ark, Protein Degradation, T1, CH3-COO(-), ASS, IGAAD, fSAP152, Sputolysin, 1-Piperazineethanesulfonic acid, DmelCG10574, TF, dApaf1, Lyw-57, GPHYSD2, Long-Term Effects, reagents, phapii, D-Apaf-1, CG9648, StF-IT-1, DFNB39, br37, glycogen storage disease 11, ur, Anionen, SLP65, carbamide, Ly-57, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Cleland, Streptomycin Sulphate, Digestion, Particles, dmax, Ultrafine Particulate Matter, reactif, Lines, SLP-65, BASH, DMEM, 3-Butanediol, NICR87, hac1, MASS, CG4299, HepG2, Fanconi-Bickel syndrome, dapaf-1S, IFNB2, H2NC(O)NH2, apaf-1, MOF, Mof, dapaf-1L, l35Dd, hepatic glycogenosis with amino aciduria and glucosuria, HEPG2, Acetamide, Polypeptide, Fanconi type, HEPES, i2pp2a, time, 1728, GLUT2 deficiency, human being, Dapaf-1/HAC-1, Reagent, NS4, Degradation, FBN, Gene, FBS, Fbs, cycE, hepatocellular adenocarcinoma cell, ACINUS, l(2)br37, PHAPII, CYCLE, Buffer, Dark/Hac-1/dApaf1, Karbamid, Hac1, HGF, Dark/Hac-1/dApaf-1, reduced, template-activating factor I, Strepto-Fatol, HEP-G2, subnumerary, ECTOL1, Harnstoff, Strepto Hefa, GF1, tiny, pseudo-phlorizin diabetes, Pro-Mega, HGF receptor binding, CYCE, D-Streptamine, reactivo, DmelCG3938, CyclE, ipp2a2, dapaf-1, 3938, dapaf, dark, decreased number, Protein Degradations, Anion, OCTD, l(2)k05007, Estreptomicina CEPA, dm-cycE, hepatopoeitin-A, DARK, glycogen storage disease type 11, taf-ibeta, Ultrafine Fiber, Long-Term Effect, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, AI838057, dArk, Dapaf-1, TAG, Hepatocyte Growth, 2-iodo-, thiol methyltransferase activity, BLNK-S, D-MEM, small, ng/ml, hepatocyte growth factor receptor ligand, igaad, Cell Lines, hepatocellular carcinoma cell, apaf1, Protein Digestion, tag, Peptide, AI875693, hepatopoietin-A, glycogen storage disease XI, Protein, I2PP2A, Dark, CyeE, SMMC-7721 cell, glycogen storage disease type XI, Dark/Apaf-I, Scatter, WMS2, teratoma with malignant transformation, HLB, hepatorenal glycogenosis with renal Fanconi syndrome, Ultrafine Particle, GSD type 11, Streptomycin Sulfate (2:3) Salt, uree, urea, l(2)35Dd, Tripcellim, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, Glycopeptide, HEP G2, hepatocyte growth factor, Particulate Air Pollutants, FBS1, Fbs1, dApaf-1/DARK/HAC-1, sample population, UREA, Protein Gene Products, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, Hepatopoietin, concentration, Estreptomicina Clariana, humid, SSKS, AA960152, Peptid, Par4, acetic acid, SCH, AA407739, CG3938, dAPAF-1"],"pubmed_title_synonyms":["HYCC1, Tcsk, Acfol, hepatoma, 4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid, determination, region or site annotation, malignant, Organic cation transporter 3, pteroylglutamic acid, vitamin B9, nucleocapsid, carcinoma of liver cells, FBP, adult hepatoma, OCT3, hepatoblastoma caused by somatic mutation, somatic, vitamin B11, supernumerary, Cell, hepatocellular carcinoma, binding site, hepatocellular adenocarcinoma, uptake, Folsaeure, HCC, primary carcinoma of the liver cells, PGA, Emt, Tsk, EMT, chemical analysis, FOLR, core, N-[(4-{[(2-amino-4-oxo-1, LYK., liver cell cancer (hepatocellular carcinoma), 4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid, carcinoma of the liver cells, PteGlu, region, EMTH, FBP1, hepatocellular cancer, pteroyl-L-monoglutamic acid, increased, positional, DRCTNNB1A, liver and intrahepatic bile duct carcinoma, positional polypeptide feature, primary carcinoma of liver cells, Hepatoma, childhood type, INSDC_feature:misc_binding, increased number, Folate, PSCTK2, adult primary hepatocellular carcinoma, HLD5, LPFS1, epithelial-mesenchymal transition, folic acid, (2S)-2-(4-{[(2-amino-4-oxo-3, pteroylmonoglutamic acid, 4-dihydropteridin-6-yl)methyl]amino}benzamido)pentanedioic acid, present in greater numbers in organism, Folbp1, acido folico, acidum folicum, vitamin Bc, acide folique, binding_or_interaction_site, Folbp-1, Folicet, carcinoma of liver, vitamin M, hepatocellular, hepatoblastoma, mesenchymal cell differentiation from epithelial cell, site, liver cell carcinoma, assay, carcinoma, Extraneuronal monoamine transporter, liver carcinoma, N-(4-{[(2-amino-4-oxo-3, cancer, liver cancer, vitamin Be, pteroyl-L-glutamic acid, accessory, N-pteroyl-L-glutamic acid"],"data_synonyms":["liquid chromatography tandem mass spectroscopy, IPP2A2, odd(Oz), ion, instrument configuration, Dm NinaC, NINA C, cleavage, CG5125, 5730420M11Rik, peptide, Polypeptides, DmelCG5723, peptido, ClvPrd, B1, ten-m, Software Engineering, Gpi-1, WMS, Computer Program, SET, Divorced, F, LCMSMS, l(3)rP126, peptides, dermoid cyst with malignant transformation, l(3)rL201, TAF-I, Nlk, phosphatase 2A inhibitor I2PP2A, Open, human protein, Computer Programs and Programming, ten-m/odz, Divorces, ten[m], Estimated, BcDNA:AT25108, DmelCG4299, set, IGAAD, Nina C, column, DmelCG10574, ppm, D1, GPHYSD2, CT16120, SGS, NK/GPI, Ten-mc, ratio, LC-MS2, Gpi, phapii, PLATEST, CG5723, LC-MS/MS, StF-IT-1, H(3)0+, l(3)05309, Thermo Scientific, results, Source Softwares, Software Tools, DmelCG5125, ACMICD, Programs, Program, Computer Applications, S-adenosyl-L-methionine:thiol S-methyltransferase activity, mOC-X, Ionen, Computer Applications Software, Computer Applications Softwares, NK|GPI, Softwares, DRONINAC, parent ion, ORG, Org, Software Applications, HLA-DR-associated protein II, instrument, DI-2, Source Software, I-2Dm, oxonium, proportionality, Gpi1-r, Gpi1-s, rate, CG4299, MASS, inhibitor of granzyme A-activated DNase, Gpi1-t, beta Trypsin, I-2PP1, Applications, TAF-IBETA, precursor ion, liquid chromatography-tandem mass spectroscopy, 2017, TAF-Ibeta, Polypeptide, i2pp2a, TMT, Proteomes, Bglap-rs1, Platelets, Gpi1s, Computer Software Applications, results., 5301, AI461847, False, FBN, Ten[m], precursor, Computer, PHAPII, LC-MS-MS, Odz, method, template-activating factor I, ECTOL1, method used in an experiment, LC-MSMS, Pgi, NINAC, Separated, CG54125, Application, Open Source Softwares, odz, proportion, NinaC, ninac, Gpi-1r, Gpi-1s, Software Application, iones, Phi, ipp2a2, beta-Trypsin, Gpi-1t, Open Source Software, 2pp2a, TPP, labeling, ions, l(3)rJ307, CG10574, CG 5125, Computer Software Application, OCTD, l(3)05301, 2PP2A, 10^[-6], Tools, taf-ibeta, odz/ten-m, dSET, dSet, peptidos, 2.2, PTHB1, thiol methyltransferase activity, Applications Software, Open Source, data, Computer Software, igaad, total expressed protein, MF, Amf, Peptide, Ten79E, Tool, polypeptide, LC/MS/MS, Software Tool, I-2PP2A, C18, Dm I-2, I2PP2A, CT42491, MFS1, Software, Data Base, NK, WMS2, teratoma with malignant transformation, Separation, CT16449, Separations, Engineering, Tripcellim, Glycopeptide, plan specification, Computer Programs, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, Applications Softwares, Ion, Isolation of Nuclei TAgged in specific Cell Types, SSKS, quotient, liquid chromatography tandem mass spectrometry, Peptid, ten(m), AA407739, l(3)00844, CG11452"],"description_synonyms":["projections, glicoproteinas, O-Glycosylated, study assay., Organic cation transporter 3, HepG2 cell, Epithelial Mesenchymal Transition, Biochemical, NK2, Hepatocyte, NK1, Hepatopoietin A, adult hepatoma, protein, neoplasm metastasis, Diagnosis, Long Term, cancer metastasis, binding site, Case Fatality Rates, dmTAF[[II]]230, Death Rates, protein polypeptide chains, Techniques, Glycoprotein, C230052L06Rik, HGFR, glycoproteins, Method, IL-6, Line, SMMC-7721 细胞, Excess Mortalities, Relapses, Analysis, protein aggregate, glycoproteine, Effect, C-Glycosylated Proteins, F-TCF, Mass Spectrum Analysis, glicoproteina, Glykoprotein, DRCTNNB1A, N-Glycosylated, Prognoses, SF|HGF, TFIID TAF250, dermoid cyst with malignant transformation, Analyses, Biology, Crude Mortality Rates, cel, Molecular, SMMC-7721, Recurrences, adult primary hepatocellular carcinoma, SF, HLD5, proteins, procedures, LYK, Methodological Studies, scientific observation, CFR Case Fatality Rate, papilla, Solid Phase Extractions, hepatoblastoma, Therapies, Age-Specific Death Rate, associated, Glycosylated Protein, Long-Term Effects, Neoglycoproteins, Therapy, Relapse, dTAF[[II]]230, anatomical protrusion, lamina, Crude Death, TAF200, Longterm Effect, flanges, DFNB39, Epithelial-Mesenchymal, TAFII-250, Procedure, somatic, HSF, TAF250/230, Spectrum Analysis, Crude Mortality, Spectroscopy, BSF2, hepatocellular adenocarcinoma, any method, TAFII250, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Mortality, HCC, primary carcinoma of the liver cells, Recrudescence, EMT, Emt, shelf, carcinoma of the liver cells, Early, region, Lines, liver and intrahepatic bile duct carcinoma, Factors, positional polypeptide feature, death rate, Hepatoma, Prognostic, PSCTK2, shelves, Glycosylated, Spectrometry, common, Mortalities, NICR87, scatter factor, Methodological, HepG2, c-Met, CG17603, projection, TAF[[II]], Methodological Study, Treatments, ridge, Solid Phase, HGF/SF, Scatter Factor, IFNB2, Mortality Rate, Crude Death Rate, Patient, HEPG2, Taf250, spine, SR3-5, Extraneuronal monoamine transporter, Mortality Determinant, SF/HGF, cancer, TMT, time, TAF230, Prognostic Factor, HYCC1, Tcsk, Disease Early Detection, d230, hepatoma, Epithelial Mesenchymal Transformation, C-Glycosylated, Procedures, region or site annotation, Effects, lamellae, Mortality Declines, NS4, Excess, Gene, dTAFII250, Prognostic Factors, OCT3, hepatoblastoma caused by somatic mutation, Crude Mortality Rate, Spectrum Analyses, protein-containing complex, mortality measurement, EfW1, process of organ, hepatocellular carcinoma, Age-Specific Death, protrusion, Mortality Determinants, Crude, lamella, period, Rate, Determinant, HGF, glycosylation, polypeptide chain, Glycosylation, dmTAF1, HEP-G2, Taf230, Gene Products, Mass, Studies, Case Fatality, GF1, liver cell cancer (hepatocellular carcinoma), Growth Factor, Technique, EMTH, Mass Spectroscopy, TAF250, Differential Mortality, study, tumor cell migration, positional, HGF receptor binding, Taf200, Excess Mortality, dTAF[[II]]250, Genetic, Longterm, Recrudescences, cell, glycoproteines, LPFS1, HPTA, metastasis, Taf1p, Extractions, labeling, ridges, Long-Term, Age-Specific, epithelial-mesenchymal transition, O-Glycosylated Proteins, Lymphokines and Cytokines, Study, dTAF250, hepatopoeitin-A, time of survival, Clients, Mortality Rates, hepatocellular, mortality rate, Crude Death Rates, mesenchymal cell differentiation from epithelial cell, liver cell carcinoma, site, Long-Term Effect, carcinoma, AI838057, Transition, TAF, laminae, Age Specific Death Rate, Hep-G2, tumor metastasis, KINDS, Hepatocyte Growth, thiol methyltransferase activity, Glykoproteine, GINGF, Transformation, Molecular Genetics, measuring, TAF[[II]]250, Hep G2, Mortality Decline, Protein Glycosylation, hepatocyte growth factor receptor ligand, protein complex, malignant, Molecular Genetic, anatomical process, Proteins, Cell Lines, carcinoma of liver cells, l(3)84Ab, Factor, BG:DS00004.13, Genetics, Extraction, Client, Cell, dTAF230, Early Detection of Disease, Case Fatality Rate, survival, hepatopoietin-A, native protein, natural protein, GGF1, p230, Tsk, Protein, Long Term Effects, Glycosylated Proteins, HGF|SF, TAF[[II]]250/230, TFIID, techniques, Epithelial-Mesenchymal Transformation, SMMC-7721 cell, Determinants, Death, flange, Scatter, Mass Spectrum Analyses, hepatocellular cancer, organ process, teratoma with malignant transformation, Taf[[II]]250, Rates, Mass Spectrum, Death Rate, TAF[[II]]230, Hepatocellular carcinoma, primary carcinoma of liver cells, childhood type, Biochemical Genetic, N-Glycosylated Proteins, INSDC_feature:misc_binding, Glycopeptide, HEP G2, hepatocyte growth factor, TAF[II]250, Age-Specific Death Rates, HGFB, Longterm Effects, Protein Gene Products, processes, process, Gene Proteins, Differential, DmelCG17603, Hepatopoietin, binding_or_interaction_site, Therapeutic, Isolation of Nuclei TAgged in specific Cell Types, carcinoma of liver, Decline, processus, Treatment, Biochemical Genetics, liver carcinoma, Par4, liver cancer, Differential Mortalities, methodology, TAF1"],"pubmed_abstract_synonyms":["projections, glicoproteinas, O-Glycosylated, determination, Organic cation transporter 3, vitamin B9, Epithelial Mesenchymal Transition, NK2, Hepatocyte, NK1, Hepatopoietin A, Glykan, adult hepatoma, neoplasm metastasis, cancer metastasis, binding site, Techniques, polisacarido, Glycoprotein, C230052L06Rik, HGFR, glycoproteins, Method, GRP1, Grp1, IL-6, FOLR, Line, SMMC-7721 细胞, Analysis, glycoproteine, present in fewer numbers in organism, C-Glycosylated Proteins, F-TCF, Mass Spectrum Analysis, glicoproteina, Glykoprotein, DRCTNNB1A, N-Glycosylated, SF|HGF, Analyses, SMMC-7721, PTPSTEP, hypoplasia, adult primary hepatocellular carcinoma, SF, HLD5, Glycane, procedures, LYK, acidum folicum, vitamin Bc, decreased, acide folique, Methodological Studies, l(2)k08110, papilla, Glycan, hepatoblastoma, Glycosylated Protein, N-(4-{[(2-amino-4-oxo-3, vitamin Be, GPH, Neoglycoproteins, ratio, N-pteroyl-L-glutamic acid, close to, Acfol, anatomical protrusion, pteroylglutamic acid, lamina, flanges, DFNB39, Epithelial-Mesenchymal, Procedure, somatic, HSF, vitamin B11, Spectrum Analysis, results, Glykane, Spectroscopy, BSF2, hepatocellular adenocarcinoma, HCC, Folsaeure, primary carcinoma of the liver cells, EMT, Emt, 3.1.3.48, shelf, carcinoma of the liver cells, PteGlu, region, Lines, liver and intrahepatic bile duct carcinoma, positional polypeptide feature, Step, CG11628, Hepatoma, PSCTK2, shelves, Glycosylated, Folate, proportionality, Spectrometry, rate, Striatum-enriched protein-tyrosine phosphatase, Methodological, scatter factor, NICR87, c-Met, Methodological Study, projection, ridge, folic acid, HGF/SF, Scatter Factor, polysaccharides, 4-dihydropteridin-6-yl)methyl]amino}benzamido)pentanedioic acid, acido folico, IFNB2, STEP, spine, Folicet, Extraneuronal monoamine transporter, SF/HGF, cancer, pteroyl-L-glutamic acid, Tcsk, HYCC1, hepatoma, Epithelial Mesenchymal Transformation, GRP1/cytohesin 1, C-Glycosylated, Procedures, 4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid, region or site annotation, lamellae, NS4, nucleocapsid, glycans, FBP, Hep-3B, OCT3, hepatoblastoma caused by somatic mutation, Spectrum Analyses, process of organ, hepatocellular carcinoma, protrusion, CG11633, cytohesin/GRP1, lamella, HGF, glycosylation, reduced, Glycosylation, PGA, subnumerary, Studies, Mass, GF1, N-[(4-{[(2-amino-4-oxo-1, Cell., liver cell cancer (hepatocellular carcinoma), Growth Factor, tiny, 4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid, Technique, EMTH, Polysaccharide, Mass Spectroscopy, tumor cell migration, positional, HGF receptor binding, proportion, glycoproteines, l(2)SH2 0323, LPFS1, HPTA, blocked, metastasis, ridges, decreased number, epithelial-mesenchymal transition, O-Glycosylated Proteins, Lymphokines and Cytokines, Study, Neural-specific protein-tyrosine phosphatase, hepatopoeitin-A, hepatocellular, vitamin M, mesenchymal cell differentiation from epithelial cell, liver cell carcinoma, site, carcinoma, AI838057, Transition, laminae, tumor metastasis, Hepatocyte Growth, Glykoproteine, small, GINGF, Transformation, Protein Glycosylation, hepatocyte growth factor receptor ligand, malignant, anatomical process, Proteins, Cell Lines, carcinoma of liver cells, stepk, Factor, Cell, near to, uptake, hepatopoietin-A, GGF1, Tsk, Protein, Glycosylated Proteins, chemical analysis, HGF|SF, core, techniques, Epithelial-Mesenchymal Transformation, SMMC-7721 cell, l(2)SH0323, Scatter, flange, Mass Spectrum Analyses, hepatocellular cancer, organ process, FBP1, CYH1, pteroyl-L-monoglutamic acid, Mass Spectrum, polisacaridos, Hepatocellular carcinoma, underdeveloped, primary carcinoma of liver cells, childhood type, N-Glycosylated Proteins, INSDC_feature:misc_binding, Glycopeptide, hepatocyte growth factor, HGFB, DmelCG11628, (2S)-2-(4-{[(2-amino-4-oxo-3, pteroylmonoglutamic acid, processes, process, Folbp1, Hepatopoietin, binding_or_interaction_site, approaches, Folbp-1, Isolation of Nuclei TAgged in specific Cell Types, carcinoma of liver, vicinity of, quotient, processus, assay, liver carcinoma, Par4, liver cancer, methodology"],"name_synonyms":["liquid chromatography tandem mass spectroscopy, LC-MS2, LC/MS/MS, HCC cell, liver adenocarcinoma cell, LCMSMS, liquid chromatography-tandem mass spectroscopy, LC-MSMS, LC-MS/MS, hepatic cancer cell, liquid chromatography tandem mass spectrometry, LC-MS-MS., hepatocellular carcinoma cell, hepatic carcinoma cell, hepatocellular adenocarcinoma cell, hepatocarcinoma cell"],"additional_accession":[]},"is_claimable":false,"name":"Hepatocellular carcinoma cell lines LC-MS/MS","description":"Hepatocellular carcinoma (HCC) ranks sixth among the most common malignancies and fourth in mortality among all kinds of cancers in the world. Recent advances in early diagnosis and therapeutics have led to improved survival of HCC patients, but the recurrence and metastasis are still main reasons for the poor prognosis and high mortality of HCC. Many researches on the mechanism of HCC deterioration have uncovered the epithelial-mesenchymal transition (EMT) as a major trigger for HCC metastasis and invasion.In this study, in order to systematically investigate the dynamic site-specific glycosylation alterations associated with the EMT process of HCC, two hepatoma cell lines SMMC-7721 and HepG2 were treated using HGF and the cell proteins were harvested at six treatment time points. Using TMT-labeling, solid phase extraction and mass spectrometry, we not only detailly profiled N-glycoproteome of both cell lines at site-specific glycosylation level, but also dynamically quantified those intact glycopeptides among six increasing HGF-treated time points. By dynamically quantifying enriched glycopeptides and proteins among six HGF-treated time points in two cell lines, we identified 20 up-regulated intact glycopeptides during the process of EMT, with the majority changed at the glycosylation level instead of protein expression level. The site-specific glycosylation change of those glycoproteins was related to the process of EMT, which was further verified by a series of molecular biology methods, mass spectrometry, and migration and invasion assay in vitro.","dates":{"publication":"2021-09-09","submission":"2020-01-09"},"accession":"PXD017033","cross_references":{"TAXONOMY":["2806551","646099","180498","511145","42249","2156843","544071","284218","327042","3633","3635","11983","430066","3636","2758385","696363","1217666","68888","1114301","55571","145263","145262","3649","34613","126957","366649","2","391619","3641","10665","68895","113636","476272","3661","1123294","42229","55583","2681304","2323","122586","3654","34607","92519","3659","10632","1432059","712938","655819","1250232","1195774","81866","196821","586722","568076","1755437","35925","3668","408169","180454","2787751","201089","225058","3674","1479564","100392","3694","2049433","445974","1420012","935293","NCBITaxon:77643","6715","67593","643867","71605","40483","1315282","69304","562716","391624","29204","277944","762376","3696","1218100","329629","2211376","39488","40479","NCBITaxon:2157","1315273","1051067","2059687","2016516","368407","1736309","698936","104782","148364","32042","929410","1061","32049","1381693","743277","32046","45351","11103","217459","216129","288671","288676","4100","694569","4101","6763","4102","1076","1277351","1316582","1358430","1417298","174633","6754","128735","6756","84030","135062","1813019","4111","929439","367110","4113","64459","1394984","32025","301270","32022","1498751","104759","4120","478861","347495","153721","1097","1652998","2790513","9803","1758543","9801","2608663","9808","13757","55518","32019","64471","114155","421932","55521","1383439","1193181","9813","9818","1026970","10699","55529","NCBITaxon:4751","8502","9833","5476","4146","5477","9825","102169","157273","9823","89764","84074","13735","1862870","5482","4153","NCBITaxon:50557","9844","67525","1000364","334147","5480","35974","13708","115466","5478","9835","322159","9838","10677","103481","9852","348780","42253","1488414","222863","47946","1571871","59919","157295","29292","1175271","9860","1488406","334249","518691","234","235","152335","9858","9859","886559","74649","9870","392021","11072","36352","7215","9874","1908","28743","4182","35024","1451139","69293","1902","593907","1901","746360","12374","746361","7226","253","60013","197221","1915","85310","588596","9895","11051","9899","7237","9897","72000","263","419610","264","266","7227","588581","568996","287375","62690","7244","2023717","201999","8570","7240","747679","274","596153","335543","1931","335541","84005","13686","150596","86662","86661","347515","36329","NCBITaxon:1763","286","287","348837","670580","271848","186536","8595","986075","105135","294","296","11009","84023","210007","348824","12336","36307","1047005","187878","945556","449447","NCBITaxon:1335626","54195","913998","78168","11901","147828","1055524","NCBITaxon:9606","135858","469008","1979153","51930","72859","300852","641140","9005","118499","526225","412133","75913","9014","38111","39442","3704","167443","1204414","3708","351581","990119","51953","2590841","3701","3702","39432","227748","62615","83558","3715","3716","333760","57267","998086","3711","3712","190650","3714","75917","2073127","262981","27457","57270","9030","9031","3728","1424337","142104","479249","11082","39412","NCBITaxon:9615","147802","69266","1006581","3735","2750454","1356638","1647520","3750","644223","669502","1293497","9054","632245","552536","51997","649908","1438992","3745","3747","264732","3760","264731","288705","595536","1416915","252740","327160","29385","1149786","479436","3755","29382","479437","225117","75299","167387","1938441","3765","93934","327159","100226","3767","42344","42345","46700","1287689","591198","46704","146479","29365","28034","28038","28035","1080348","179392","1126212","295027","1131","6819","1126","526997","102862","10760","159736","1143","1140","981087","1355477","43658","1424507","229533","79698","204232","124223","321803","369822","34708","1645733","1858897","1654675","99287","77020","38293","1412529","5508","1148","1744888","643745","2649997","283035","718308","5507","176299","707678","92683","70415","1562887","651388","563924","56115","2086595","5516","5518","113549","1432137","159749","535026","1432138","58781","707683","194963","401614","28005","31646","104660","381518","45474","48500","97476","97477","1180","51240","1748418","55601","555479","204274","2014887","1105325","329726","1005941","28909","316435","1211604","9900","13894","382835","4232","4233","1082934","1220585","604162","9913","112273","170187","9915","429131","267818","1871049","316407","299467","303","337330","485264","638301","1306413","9925","306","4236","1211620","652616","103372","8612","9940","207340","115357","652611","1147161","338654","312017","253237","1255232","9935","316","317","NCBITaxon:11084","9938","41063","267872","8623","219334","8620","8621","160791","392227","681196","1255228","149539","321","322","323","34774","1218275","329","1757312","9948","8618","1408434","103351","9963","1392488","115338","115339","330","439375","56992","8626","339","1120948","8624","157183","9975","8644",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