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Luna S, Malard F, Pereckas M, Aoki M, Aoki K, Olivier-Van Stichelen S. Studying the O-GlcNAcome of human placentas using banked tissue samples. Glycobiology 2024 34(4) 38253038
Abstract:
O-GlcNAcylation is a dynamic modulator of signaling pathways, equal in magnitude to the widely studied phosphorylation. With the rapid development of tools for its detection at the single protein level, the O-GlcNAc modification rapidly emerged as a novel diagnostic and therapeutic target in human diseases. Yet, mapping the human O-GlcNAcome in various tissues is essential for generating relevant biomarkers. In this study, we used human banked tissue as a sample source to identify O-GlcNAcylated protein targets relevant to human diseases. Using human term placentas, we propose (1) a method to clean frozen banked tissue of blood proteins; (2) an optimized protocol for the enrichment of O-GlcNAcylated proteins using immunoaffinity purification; and (3) a bioinformatic workflow to identify the most promising O-GlcNAc targets. As a proof-of-concept, we used 45 mg of banked placental samples from two pregnancies to generate intracellular protein extracts depleted of blood protein. Then, antibody-based O-GlcNAc enrichment on denatured samples yielded over 2000 unique HexNAc PSMs and 900 unique sites using 300 μg of protein lysate. Due to efficient sample cleanup, we also captured 82 HexNAc proteins with high placental expression. Finally, we provide a bioinformatic tool (CytOVS) to sort the HexNAc proteins based on their cellular localization and extract the most promising O-GlcNAc targets to explore further. To conclude, we provide a simple 3-step workflow to generate a manageable list of O-GlcNAc proteins from human tissue and improve our understanding of O-GlcNAcylation's role in health and diseases.
O-GlcNAc proteins:
TRGV5, TVBL4, HV320, TM275, MRCOL, EXC1L, TVB74, TVBK3, FEZF1, DEND3, MTMRB, PI4P2, POTEF, ARB2P, U17L3, LIRA5, S22AV, O6C75, SHSA7, TCPQL, SIG16, O4C45, P12LL, D11L8, ARG33, CD15L, YQ037, ZN487, TDR15, ERVV1, NACAM, ADAS, TAF4, CLIC1, MATN2, LORF2, ACACB, ARI1A, NCKP5, IRS4, ADA10, ZN609, SC16A, MCF2L, ERC2, ARHGB, FANCG, TNC18, MRP5, SIA8E, DDX3Y, MEFV, TET3, TTI1, SI1L1, SERA, M3K13, SNUT1, MTSS1, ZN208, HXA3, HNRPR, IF4G3, FOXO3, KCNQ2, LAT, BUD23, MYO1B, NRDC, S28A2, KIF1C, ADCY3, JIP4, SI1L3, TRAK2, L37A3, OPA1, GANP, KDM1A, FZD6, PLIN3, F262, SH21A, MMP20, ROCK2, LRP5, GLRA3, ZN217, USH2A, MYCB2, NU155, P3C2G, NALF2, CABYR, CDKA2, TRIO, C1QRF, CBPD, OR7C1, RECQ4, RECQ5, BAIP3, ATG12, NFASC, SRBS2, PCF11, ABLM3, SC31A, KCNK2, UBR5, AGFG2, SPN1, UBE4B, SCEL, CAC1H, RTN3, EPN2, STBD1, OR6A2, KCNH1, SMC2, TACC2, ZBT7A, CLD9, AGRL2, GLP2R, LGI1, MBD3, ANGT, EGF, IL2RA, LV223, IGHG3, IGHG4, IGHM, CO1A1, CO2A1, CO3A1, CO4A1, FETA, HMDH, A1BG, TBB4A, CP1A1, RPN2, ALDH2, HEP2, CO5A2, INSR, GELS, TY3H, ACBP, LDHB, NFM, CATD, TBB5, CBG, PFKAM, INHBA, CO4A2, IL6RA, PKHD1, HXB5, DLDH, IFI6, DANCR, DU4L4, O13C7, CC192, EFCE2, TZAP, LYAG, TGFB3, HSP7C, PSG1, MPRI, PRPS2, FGF5, COBA1, CO6A3, RLBP1, KCRU, MYH1, HEM1, K1C13, CO6, COBA2, ENPL, ATF2, VAV, IGLL1, PGCA, ZN823, HSP76, JUND, PFKAL, EGR1, XRCC1, K2C4, CADH2, TSN8, LFA3, ITIH1, TYPH, PSB1, CO9A1, C4BPB, NEBU, PRPS3, FLNA, NF1, MUTA, TENX, IDS, PROZ, KS6B1, PTPRZ, MYL9, CO8A2, ITA3, 3BHS2, SYVC, PON1, VATL, CD82, MAP4, TPP2, EPHA8, CO4A5, MPIP1, V2R, SC6A1, CLIP1, HXD11, 3HIDH, PRDX2, DSG3, C2TA, ACSL1, CSTF2, MRP1, MCM7, BMP8B, HSP74, TRY3, PCGF2, ADML, ADA1A, GGT2, VATA, HSPA9, COFA1, PK3CB, PI4KA, CNDD3, THIM, MAGAC, ABCG1, KI67, NOP2, UTRN, PA24A, OR1D4, TNFL6, SC6A8, IREB2, PK3CG, RPIA, SYCC, RBP2, RGS3, GSK3B, MNX1, F10A1, LRBA, TCPD, SMCA2, GALK1, IRAK1, DHB4, NEK3, ROA3, MYOM1, IMA1, JAK3, ZN142, EFNA4, SMTN, SC24C, ATX3, SYYC, HSP72, RD23A, GYS2, LMIP, SYMC, DPOE2, HDAC4, PER3, BACE1, BCAR1, CORO7, KCNKA, SESN2, FOXL2, ATS20, C1QT8, SIA8F, RS6, VPK21, POK7, HBA, RNF4, IRX4, DEN2B, SSBP2, RT05, EFNB1, AT8B2, EM55, HXC5, PLCB2, PSG9, E2F1, CO4A3, OCRL, NAAA, CO7A1, DSG1, MUC3A, GUC2D, AKA12, DYST, CREM, ROM1, KIME, COAA1, COEA1, KDSR, ZO1, SOS2, PP2BA, DHX9, CACB2, GOGA3, CLM6, SPIR1, EP300, AHNK, KLH30, MN1, SIAT6, WASC5, KCMA1, RB40B, DLG1, NFAC3, ABR, STK4, CSN1, IFT88, KLF10, RFA4, PSMD2, MMRN1, M3K1, IFIT5, PDE3B, ADAM9, BIRC2, OLIG2, CUL4B, DYR1A, PTC1, THOC5, CAYP1, CDK13, CO4A6, NID2, VEZF1, DELE1, BTG3, DYHC1, NPAT, E2F2, FLNC, LRC32, NF2L1, FAT1, HABP2, SCN5A, ITIH4, TRIPC, NCOA6, MBTP1, PTCA, ICAM4, MYPC3, COJA1, NAA25, CND1, ACAP1, SETB1, RRS1, RYR3, KS6A1, SURF1, TAF7, OR7A5, PCH2, MED1, JHD2C, U2AFM, HERC1, CAC1E, B2LA1, MIA, QPCT, RTN1, PPR3A, SIA4B, PTPRN, SYT16, COOA1, DOK7, CSPP1, INF2, MICB, KI26B, BLTP1, MGAL, SC5A9, RPEL1, TMM44, SMTL2, COSA1, KLH38, FR1L6, S4A8, RGL3, WDR72, CCD14, C2CD3, HYDIN, SRCRM, GREB1, SEZ6, DHB12, SETMR, SDK2, DCAF6, ACTMP, ACBG2, ESCO1, FREM1, PWP3B, BRD10, MTX3, AKAP4, PREP, RRP12, FRPD3, DOP1, SNP47, MUC21, SAPC1, SNPC4, EYS, MRP7, RBM20, ZFY27, CAMP1, RM02, ADIPL, LITD1, KANK4, TTBK1, MTCL3, BIG3, STPG1, RAIN, RIF1, OBSCN, MRCKA, EF1A3, AGAP9, TCRGL, RSBN1, C1QL3, DEN4C, RRAGB, USPL1, EST4A, RN123, RN213, EGFLA, TENS2, SAXO2, ICE2, MAP1S, B3GNL, RPGP2, NR3L1, USF3, ZFY26, CR063, S31H1, WWC2, BLT3A, MRCKG, RGPA1, NADE, CPZIP, ALKB2, DHX57, MSD2, ACSM6, BGP11, ZN549, CCD62, S2534, TXD11, XKR2, GP179, TRAF7, CORO6, ARL9, ANR11, CRTC1, CSPG4, CP20A, EST3, PRS57, XKR5, PAMR1, ITIH6, FAT4, NHLC1, BCOR, IGS10, GGYF2, ATL5, EMAL6, NFXL1, ALKMO, NBEL2, DMP46, NBEL1, RFLA, CFA47, TPGS1, UBN2, MROH5, TPRG1, PHLP2, ACD11, UBP54, UBP43, UB2R2, MD13L, KNDC1, SND1, TEDC2, NDUF7, FA2H, VASH1, GRP2, CXXC5, ZCCHV, GLUCM, VP35L, MIER3, CA2D4, ZFY16, CSMD3, LFG1, PK1L2, GDF7, HEAT3, MDGA2, BRAP, MUC19, RBBP6, SH3R1, RAB44, TAF8, TARSH, VP13B, TMED4, UBP37, K1328, ALPK2, ACOT1, CN023, PABP2, MTA70, LYRIC, BCL9L, GGN, CASZ1, VASH2, MOGT3, NAL14, NLRC5, HEAT4, RLGPB, CIR1, MICU3, HOGA1, GA2L3, PRSR1, ZGRF1, THNS2, C2CD5, KR191, TMTC1, AHNK2, MGAP, ANKH1, LMTD2, ZC3H3, SP8, MILK2, REM2, ELMD2, CORA1, MAML2, DSEL, MIER1, INT1, SCML4, LRC43, CIART, CLIP4, CMYA5, PRR18, T151A, PAQR4, FBXL6, SRBD1, NKAP, TBC19, MEIOB, IGSF1, TEX26, ARFG2, ARI2O, SIGL1, DCBD1, AMER3, ABTB2, SYT2, TRIML, DAAF3, LMTD1, LMBL4, FANCB, NHLC2, DRAXI, SIDT2, DHB11, P5I13, CAMKV, MACA2, SMG8, RN214, HMCN2, CC168, RB15B, TNR6A, BHE23, DIK2A, CC112, ZSWM2, ZMIZ2, COMA1, MYRIP, NEK11, O4F15, O51S1, OR6T1, OR6K6, O10R2, OR1FC, LIRB1, KI18A, NPL4, MUC7, ALMS1, LKAM1, MO2R1, DSCL1, GTR14, GRP4, ACTT1, CHD5, DMXL2, DLG5, HAVR2, LMX1A, SH3R3, FBF1, FNIP1, ZN526, SETD7, COG1, FRS2, LMO7, TCP11, NELFB, PALLD, ATRIP, STON2, AGRV1, CNKR2, MUC16, ASB15, TITIN, S39A7, NR4A3, MAML1, HS105, AKAP1, RYR2, TENR, RREB1, CBP, PRG4, GLMN, DVL3, TNR25, SBP2L, NKD2, POP5, P33MX, SOSB2, RPE, CR3L1, MSI2H, NXPE2, SGTB, TV23C, DTBP1, MCRS1, MISP3, LRC46, CFA36, FUBP3, BOD1, HPDL, LRIG1, M4A14, DYH8, VPS39, SPTCS, MAML3, ZN333, LCOR, MY15B, S35E1, PHAR3, P12L2, ALPK3, IFT74, PRRC1, CCDC7, DNHD1, HARB1, CFA44, SPT33, TTC14, HUTU, LRRC7, QRFPR, GPR78, NOE3, PGRP2, ARHGH, GBP4, SIG12, PP1RA, DEPD7, PHF12, MAGI1, TAAR9, MED15, GCP5, HMCN1, CRML, WDR24, S22AC, TM209, CP2S1, NIBA2, STAC, AGAP2, PLIN2, PKP4, PI3R4, PMYT1, EPYC, LYST, COCA1, SMAD5, ZNT3, TEP1, TBL1Y, SLF1, SYT15, TIRR, PSF3, ZN649, CRDL1, ZSA5A, TBB2B, TRPM6, C1QT4, PINK1, COPA1, TEX15, AN30A, PECR, K1671, CDHR2, GSDMC, TRI55, PITM3, CPEB1, BARH1, IRX2, CFA74, TANC1, LNP, ASXL3, SRCN1, WDR33, ARP3C, BRD8, RBM38, I2BPL, TRPV6, S6A17, GBA3, CAD23, VPS11, SLK, HIPK2, ATS10, E41LB, UBQL3, KDM4C, SEM6C, RIBC2, PDZD7, AT133, MT21D, CCNP, GORS2, PANK3, SPE39, AGO3, RPA2, S28A3, LY9, TENS1, TM165, NCKX3, MUC5B, CAN10, SPON1, NCOA5, TANC2, PLXA4, TRI39, PDE11, WDR6, MLXPL, OSGEP, UBN1, MEPE, ANO2, BIRC6, ARHG4, KCNQ5, MXRA5, 4ET, SH2B1, SNRK, KCNH7, SIA7A, LRC4B, MDN1, FX4L1, ZBT40, DECR2, SPS2L, HAUS2, AKIP, OXSM, SIR5, ZDHC7, ING3, SNTG2, SO1C1, DACT1, CELR1, CELR3, ERAP1, PDXL2, DTL, PA2GE, MYOF, CNOT2, LRP1B, FOXJ2, AKA7G, YP008, SIRPG, PHRF1, PLCE1, ZSWM5, DYH2, JCAD, FPRP, CT2NL, CHD7, HTR5B, F135A, UNC79, RRBP1, UBP35, KANL3, NYNRI, ZN219, HNF6, MYO1A, DBF4A, KCNN3, AAKG2, RPGFL, MED13, VAX2, ENPP5, DP13A, BORG2, TLK1, PO2F3, MUC12, CDV3, TEN1, TRPC5, PADI1, DEN2A, F184B, INO80, MRTFB, ZBT21, HECD1, ZMYD8, CAPS1, COHA1, KMT2B, BARX2, PCDGK, PACN2, ATS8, BSN, LHX6, MACF1, PHF8, IQEC3, LIMC1, ANR26, UBP24, CBPC1, TUTLB, SRRM2, CNTN6, CHKB, RT33, ZN652, SL9A8, ANKR6, PKHA6, SIK3, YBOX2, COG6, ZBT32, LSM2, PHOCN, RTCB, GRIP1, WNK2, LMBL1, DMXL1, ARIP4, MTCL1, CRBG1, PRC2C, YTHD2, PCDB7, SPO11, CD2AP, ENTP2, CERT, MRCKB, NR2E3, HEBP2, NCOR2, COX11, AP1M2, NCOA3, M3K4
Species: Homo sapiens
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Vang S, Helton ES, Guo Y, Burpee B, Rose E, Easter M, Bollenbecker S, Hirsch MJ, Matthews EL, Jones LI, Howze PH 4th, Rajasekaran V, Denson R, Cochran P, Attah IK, Olson H, Clair G, Melkani G, Krick S, Barnes JW. O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis. Frontiers in immunology 2024 15 38665916
Abstract:
Idiopathic pulmonary fibrosis (IPF) is a chronic pulmonary disease that is characterized by an excessive accumulation of extracellular matrix (ECM) proteins (e.g. collagens) in the parenchyma, which ultimately leads to respiratory failure and death. While current therapies exist to slow the progression, no therapies are available to resolve fibrosis.
O-GlcNAc proteins:
NUD4B, GAL3B, UBA6, HACL2, SPD2B, NBAS, SBNO1, VP37C, CNOT1, ZN316, DDTL, ZSWM8, P121C, GNAT3, EIFCL, C2D4D, IGLL5, NACAM, DNS2A, ADAS, PDLI1, BACH, MYO1C, AIP, GTPB1, AP3B1, PSD11, PSD12, PSMD9, ATOX1, CBX4, PGRC1, SPT5H, TAF4, DFFA, CLIC1, TR11B, EIF3F, ODPX, MATN2, QSOX1, WASL, IPO5, EMAL1, IF2B3, DNM1L, MANBA, PLOD2, MEIS1, PSDE, ZN593, IMA4, BCL9, PESC, NOP56, DDX3X, CCN1, IMA3, MA2B1, SCD, PLPP3, ARI1A, TRAD1, HSPB6, COPE, IF1AY, CCS, DVL2, TOR1A, P5I11, ANM5, NHRF1, TPP1, TCRG1, NRP1, PSA7, SCAM3, ML12B, HGS, MYPT1, GAK, HNRDL, XPO1, ZN609, SC16A, PLXB2, SR140, SET1A, SYNJ2, PUR4, NPC1, TBX3, ARC1B, ARPC2, ARPC3, TIF1A, NKRF, CASC3, RER1, SURF4, SPTC1, SPTC2, OGT1, PMM2, PPM1G, SHIP2, EIF3D, EIF3H, IPO8, STX7, MOT4, MRP4, P4HA2, NUP42, ARPC5, CLOCK, TPSN, KDM6A, DHX15, ASAP2, PRP4, SERA, DC1L2, PSMD3, RFOX2, PAPS1, SNUT1, DAPK3, TGFI1, CTIF, M3K7, MCA3, HNRPR, PRPF3, TXNL1, TPD54, EMC8, SYNJ1, IF4G3, ARK72, E41L2, B4GA1, FOXO3, RNF13, DENR, XPOT, PLRG1, ZN207, NDUA2, BUB3, ACTN4, AP1G1, SNG2, SGTA, SYNC, KRT86, MYO1B, CPSF5, LANC1, U3IP2, AKAP8, NRDC, CALU, EDIL3, SAHH2, EXTL3, MED14, SMCA5, TRAK2, GANP, FADS1, PEPL, NRP2, MA1A2, ACSL4, SNX3, OGA, HNRPQ, TPST1, NEMF, GREM1, PLOD3, SEP15, TSN3, PLIN3, MAFK, UGDH, CTND1, DPM1, USO1, RT14, H2B1K, PRAF2, DKC1, IF2P, DNJA2, BRD4, MITF, SRGP2, WDR1, ROCK2, CPNE3, PHF2, T22D2, PP6R2, CREST, ANR17, GGCT, NDUS2, ZPR1, DUS11, NIPS2, SEM7A, LX12B, TBCA, VATG1, H2AY, FLNB, NCOR1, NDUS6, CISY, SPAG7, SC22B, DEAF1, PR40A, MPPB, PSIP1, ERLN1, CLN5, CLD11, SF3B1, CSDE1, WBP4, PRKRA, LYPA1, ERAL1, U520, TIPRL, CRTAP, EIF3G, EIF3J, CBR3, FACE1, IDHC, ATRN, STAM2, PIAS1, PIAS2, DNJC8, SPF30, ATP5H, TRIO, CBPD, KT33A, KRT34, KRT36, RL1D1, WFS1, CLPX, STC2, PDE5A, SRP72, DDAH1, B3GA3, MTA2, AL1A2, TOM70, TOX4, SC24D, PHF14, CSCL1, TOX, SUN1, ERLN2, PRP6, NFAT5, GLSK, SC31A, CSTN1, YIF1A, AGFG2, SCAF4, ZFPL1, ELP1, NDUB8, LETM1, ZRAB2, LC7L3, VAPB, MPZL1, NDUAA, FKBP9, 6PGL, PAPS2, SMC2, IPO7, AGM1, SVIL, AHSA1, PSMG1, NSA2, G6PE, SC24A, SC24B, ETHE1, ACSL3, CNOT4, EYA4, K2C75, OXSR1, AP2A1, WIZ, STAU1, BAG2, BAG3, AIFM1, LATS1, BPNT1, FADS2, DDAH2, ABHGA, TXD12, FBLN4, RECK, NUDT3, NDUBA, CLPT1, TOM40, ACL6A, CYB5, LDHA, DHE3, NB5R3, GSHR, COX2, PNPH, HPRT, AATM, EGFR, PGK1, C1R, PLMN, UROK, TPA, ANT3, A2MG, CO3, CO5, TIMP1, CYTA, RASN, LDLR, TGFB1, IGHG1, IGHA1, HLAB, CO1A1, CO3A1, CRYAB, K1C14, K2C6A, LMNA, APOA1, APOC3, FIBA, FIBB, FINC, AMBP, FETUA, FETA, VTDB, TFR1, TRFE, TRFL, CATA, RAF1, GBA1, FUCO, ALDOA, ANXA1, APOB, GCR, PRIO, SODM, OAT, HRG, THY1, K2C6B, K2C1, G3P, HLAA, CPNS1, AMYP, HSPB1, RPN1, RPN2, GNAI2, AT1A1, A4, ARGI1, APOD, ALDH2, ITB3, S10A8, PAI1, ADT2, IF2A, RLA2, RLA0, JUN, LA, HEP2, ITB1, K1C18, K2C8, CO5A2, DCUP, LCK, GELS, PTMA, CDK1, ATPB, S10A9, S10A6, IF4E, ENOA, G6PI, NPM, ITAV, HEXA, H2B1J, GDN, HYEP, LDHB, PGK2, PDIA1, H10, CATD, ANXA2, CAN1, TBB5, TRY1, PGS2, SAP, HEXB, CATL1, PROF1, APT, SYEP, CATB, HS90A, HNRPC, LAMB1, TPM2, FUMH, TSP1, SP1, CO1A2, ANXA6, 4F2, PFKAM, HS90B, SRPRA, ASNS, ODPA, CY1, RU2B, RU17, ITA5, NFIC, VIME, A2AP, RS17, GNAI3, ANXA5, K1C16, STS, RSSA, CD63, FGF2, GSTP1, RU1C, LEG1, DHPR, HMGB1, SPRC, TPM1, CLCA, ANXA4, CN37, PGFRB, DLDH, ROA1, PARP1, UCHL1, LKHA4, ALDOC, CO4A, H2AZ, UCRIL, ATX1L, POTEI, ZN865, ZN888, INAM2, HS71A, GLI2, LYAG, HLAC, H14, ODP2, THIO, PPGB, MGST1, KAP0, ESTD, CH60, CLUS, BIP, LAMC1, PPAL, HSP7C, UMPS, ODPB, ODB2, PYGB, RALA, LAMP1, ACADM, FGFR1, TOP1, G6PD, PYC, C1TC, MPRI, ADHX, SRF, PABP1, PCNA, HARS1, CO6A1, CO6A2, CO6A3, ADT3, IMDH2, TPR, ACTN1, PEPD, XRCC6, XRCC5, COX41, IFM1, LAMP2, RINI, CSPG2, EF2, K1C13, K2C5, PDIA4, P4HA1, TCTP, HLAE, PLST, ACPH, ETFA, KAP2, ENOB, CD59, MIF, CD99, GLU2B, FPPS, NID1, AK1A1, KPYM, ENPL, RSMB, IDE, PO2F1, HNRPL, SYDC, PLAK, ALDR, AMPN, PVR, ERF3A, B4GT1, EZRI, ATF2, UCHL3, FOSL1, FOSL2, NDKA, GNS, ZEP1, ARSB, RS2, ITF2, TFE2, DESP, RFA2, CD44, CBR1, CREB1, PGFRA, BGAL, H15, H13, H12, NCPR, AT2A2, FAAA, STMN1, NAGAB, AATC, KPCA, JUNB, ITA2, ASM, UBF1, HXB6, ATF7, CAN2, DESM, CEBPB, PYRG1, EGLN, DDX5, LEG3, IBP3, TCPA, PTN1, IBP2, RL35A, ARF4, RL7, EGR1, VINC, SON, RL17, PGAM1, RCC1, ATF1, NUCL, HXK1, E2AK2, SPEE, CSK22, RXRA, ITIH2, ITIH1, NFKB1, FST, IF2B, ANXA7, CD22, RAB3B, RAB5A, PSB1, MPRD, COX5A, LMNB1, HXA5, IMDH1, CO5A1, FILA, GSTM3, VATB2, CSRP1, FLNA, ACOHC, 5NTD, VDAC1, PGS1, SDHB, COMT, TGM2, PIMT, FBRL, PUR2, PUR6, SCP2, UBA1, NDKB, SPR1B, SPR2E, ROA2, RFX1, CBL, IBP4, QCR2, TGM1, FBLN1, PGH1, ITA6, SFPQ, PPIB, MAOM, SYWC, RS3, SAHH, COF1, IF4B, AT2B4, DGKA, GATA2, CPT2, KTHY, RIR1, EF1B, IBP5, PPAC, THIL, TENA, MYL9, RPB1, PAR1, MCM3, NFYB, ZA2G, THTM, RS12, TYY1, DNJB1, DNJB2, ATPA, PSA1, PSA2, PSA3, PSA4, ITA3, MOES, DDX6, DNMT1, U2AF2, RL13, IVD, HMGB2, PTBP1, SYTC, SYVC, EF1G, FKBP2, STOM, 1433T, DPP4, ARNT, RL10, APEX1, PYR1, CALR, MAP4, CALX, PSB8, PSA5, PSB4, PSB6, PSB5, ABCD3, ITPI2, LYOX, ELK4, NDUS1, MK01, GRN, AMPL, TPP2, IMPA1, CCN2, EPHA2, EPHB2, TKT, SPB3, RBMS1, PML, EF1D, MARCS, GNA11, AL4A1, ERP29, PRDX6, BLVRB, PRDX5, PRDX3, ATPD, RL12, ECHM, PEBP1, PDIA3, 2AAA, CDC27, T4S1, NMT1, PURA2, UFO, AMRP, TSPO, PUR8, CLIP1, SORCN, CTR1, AL1B1, RPB2, LCN1, SDHA, GDIA, S10A7, METK2, RIR2, TIA1, ZEP2, DNJA1, AKT1, QCR1, 3HIDH, PUR9, HNRH3, HNRH1, CASPE, 1433B, STIP1, S10AB, PRDX2, P5CR1, GBP1, ELF1, RL9, KINH, DUT, MRP1, MCM4, MCM5, MCM7, CD68, GLYM, HSP74, PROF2, CTNA1, CTNB1, PHB1, RADI, RFA3, RFC2, RL22, CBS, K1C9, FBN1, FBN2, IRS1, MYH9, MYH10, COPB2, ADDA, BASI, TIMP3, FUS, NU214, DEK, SOX5, GLRX1, PRS7, MP2K2, ATPG, RL4, LONM, PGM1, PP1G, PEDF, ODO2, GPX4, SRP14, NUP62, TAGL2, TALDO, ETFB, RBMX, VKGC, VATA, HSPA9, IF4A3, RS19, RL3, COIA1, OST48, AN32A, FEN1, CAPG, IL6RB, TXLNA, TCPZ, NNMT, RL13A, STAT3, MDHC, MDHM, ECHA, IF2G, ETV6, WNT5A, BUD31, NAA10, CSK, GARS, SYIC, KPCI, LAP2A, LAP2B, MTREX, HUTH, CASP3, RS27, HELZ, LPPRC, THIM, RL35, PCP, ECE1, LIS1, MUC18, MATR3, SSRA, RANG, PRS6B, PPIC, VDAC2, CBX5, UBP5, RAGP1, RECQ1, NOP2, CRKL, BAG6, NSF, NOTC1, MP2K3, RL27A, RL5, RL21, RL28, RS9, RS5, RS10, MAP1B, YAP1, UTRN, IQGA1, STT3A, CAZA2, CAPZB, SYQ, RL29, LEG7, TISD, ATPO, LIMS1, PPCE, MAOX, RFX2, RFX5, SOX9, COPD, LSS, PP2BC, CD151, PRC2A, TCPE, NEST, HSP13, KC1D, IDHP, PIPNB, PAXI, NR2C2, AL9A1, RL34, LMAN1, NASP, FAS, CDK8, TCPG, EFTU, AL7A1, SRP09, PCY1A, SYAC, SYCC, SYSC, MA2A2, PSB2, MCM2, COMP, ACADV, YLPM1, TMEDA, RBM25, NUMB, HINT1, NU153, RBP2, GSK3A, TAF6, 5NTC, SEPP1, GUAA, IDH3A, MMP14, GDIB, EMD, CPT1A, SERPH, PDLI4, F10A1, VASP, DYN2, MAP2, TOB1, CDK9, BCAM, PPT1, RL14, TCPQ, TCPD, ANX11, PAPOA, RAB5C, RAB7A, RAB9A, DAP1, RT29, SMCA4, IDH3G, SSRD, BAP31, DHB4, PSMD7, SPHM, CLCN5, KS6A3, HDGF, LUM, CNN1, NDUA8, ROA3, 6PGD, HNRPM, IMA1, NCBP2, GDIR1, AGFG1, HNRPF, STAT2, TF2AA, MSH6, ZN143, RBM5, SPSY, THOP1, CAZA1, CRIP2, NUP98, BIEA, TXTP, PPP5, ACLY, FOSB, MAP11, SUCA, PGTB2, COPB, COPA, CATC, RPAB4, MOT1, SC24C, TCP4, SYRC, ATX1, ATN1, CA2D1, SYYC, UBP14, AAKG1, HSP72, BCAT1, AT1B3, RD23A, RD23B, ANAG, KAD2, P5CS, SNAA, IF5, PSMD4, DRG2, XPO2, TERA, ECHB, MANF, AF10, DSRAD, LAMB2, CAD11, CAD13, SEC13, NH2L1, PSA, HNRH2, SCOT1, EIF3B, BID, SYMC, ITA1, MAZ, ATP5E, ATP5I, HDAC4, IF6, CTBP2, BCAR1, TMM33, PCBP3, NU107, MTPN, ARPC4, TPIS, EIF3E, SC61B, PP4C, GBRL2, MYL6, ACTB, IF4A1, RS20, PRPS1, PSA6, S10AA, CDC42, DEST, SPCS3, SRP54, RAB2A, RAB10, UBC12, UBE2K, UBE2N, RAB14, ARP3, ARP2, ARF3, ABCE1, RAP1B, RS3A, RL26, RL15, MGN, RL27, VA0D1, RL37A, RHOA, CH10, S61A1, LYSC, STXB1, B2MG, DAD1, NPC2, COPZ1, SUMO2, UFM1, NTF2, HNRPK, 1433G, RS7, PP1A, PP1B, PRS4, PRS8, RS8, RS15A, RS16, 1433E, RS14, RS23, RS18, RS29, RS13, RS11, RUXE, RUXF, SMD1, SMD2, PRS10, RL7A, RB11A, ERF1, CNBP, YPEL5, RS4X, PP2AB, ACTA, RL23A, RS6, H4, RAB1A, RAN, RL23, RS15, RS25, RS26, RS28, RS30, GBB1, RBX1, GBB2, RL30, RL31, RL10A, RL32, RL11, RL8, PPIA, FKB1A, RS27A, GRB2, RAC1, AP2B1, VAMP2, GNAS2, 1433Z, SUMO1, RL38, SKP1, RS21, IF5A1, RACK1, ACTG, ACTH, PP2AA, YBOX1, SC11A, CSK2B, TPM4, UB2L3, EF1A1, TBA4A, TBB4B, CSK21, HBB, NOMO3, HBA, F193A, IGBP1, SHPS1, SERB, PITX1, IF4G2, GTF2I, CNTP1, PHC1, TCPB, RAE1L, GSTO1, PRKDC, MAP1A, NUCB2, DCD, SSBP2, SARNP, RL24, RL36A, SMAD3, ERH, RHOG, RL19, SRSF3, FOXK1, DAB2, FBLN2, PGBM, XIAP, RBM10, RBM3, CYC, S25A3, VIGLN, PURA, BORG5, CLH1, FKBP3, REEP5, DHSO, HNRPU, U2AF1, SPTB2, TIAR, SET, SRSF2, FOXK2, RUNX1, AMPD2, FABP5, CAP1, K22O, HMCS1, LAT1, EXOSX, OTUD4, PFKAP, EWS, PLCB3, ROR2, TAGL, MEF2A, ODO1, DSG1, SP3, RL18A, FKBP4, PLOD1, NUCB1, RL6, TOP2B, CREB5, AKA12, M2OM, DYST, CAV1, KMT2A, LMNB2, UPAR, TF65, GLGB, IF4G1, K1C17, NOTC2, TLE4, LGUL, AK1C1, 1433F, PLP2, CSTF1, UBE3A, FAK1, CALD1, COEA1, PUR1, GFPT1, SUH, MEF2C, GABPA, GABP1, PRDX1, RL18, CKAP4, ZO1, KHDR1, BAX, KLC1, ACK1, LRP1, SRSF1, RHG01, TLE5, TGM3, PP2BA, DHX9, QOR, GOGA3, GOGA2, LG3BP, DSC1, CD47, PPID, SSRP1, NSUN2, RBBP4, NCBP1, MGT5A, EP300, AHNK, IFFO1, INCA1, NEXN, MGAT2, GALT2, GALT1, AP1B1, CPSF1, MPPA, SCRN1, NU160, SCAP, SRBP2, TWF1, ASPH, FBLN3, TROP, BPTF, FSTL1, GRSF1, NFIA, SFSWA, SF3A3, SEPR, TP53B, AIMP1, ILF3, LMAN2, EPS8, TRAP1, TAF10, ECH1, STRN3, CDC16, FLII, CSN1, MTAP, AAPK1, EI2BE, TADBP, ROA0, AIMP2, PRDX4, PAK2, CBX3, PSMD2, TBX2, SRSF9, SRSF5, SRSF6, TIF1B, G3BP1, SG2A2, PTK7, PABP4, EIF3I, CTBP1, UB2V1, DC1I2, ILK, NNTM, TCOF, S39A6, SF3B2, ADAM9, TMED1, LSAMP, MYO9B, GAB1, SMAD4, PICAL, MAMD1, SQSTM, TBB3, ASAH1, PRP4K, PIN1, RIPK1, HDAC1, KCC2D, DCTN2, TRA2A, SNX1, CUL1, CUL4A, CUL4B, DYR1A, FCL, FHL1, FHL3, CD166, RUNX3, SPTN1, PKP1, DX39B, BLMH, TBB2A, IDI1, RUNX2, PEBB, NFYC, CDK13, CKAP5, COTL1, HNRPD, SCRB2, NID2, DAG1, VEZF1, EIF3A, UBP2L, SCRIB, GIT2, MLEC, TTL12, FHL2, DPYL3, DCTN1, DYHC1, SRC8, RCN2, TRI25, FLNC, FKBP8, FZD2, GAS6, CAPR1, RBM39, FAT1, SEM3A, MCM6, DSC3, PUM1, EPN4, SMC1A, RRP1B, NCOA6, GSE1, GANAB, 2A5D, LBR, MVP, LTBP1, LTBP2, MEF2D, CHD4, LASP1, ARI5B, PTGR1, NC2A, ZN638, IMB1, NOLC1, NUMA1, K2C72, CND2, PSMD6, SEPT2, SART3, CND1, U5S1, R3HD1, TRAM2, RB3GP, SYK, IF4H, BRD3, POSTN, OXA1L, EEA1, PDIA6, PA1B3, PCOC1, PLEC, IPYR, TEBP, NONO, RBBP5, RCN1, PCBP1, PCBP2, RHEB, DHC24, SF3B3, PUM3, DLGP5, RSU1, CNN3, SF3B4, SF3A2, RBMS2, SC23A, SF3A1, CDSN, SSXT, BGH3, NCOA2, TRAM1, SF01, MED1, JHD2C, TRIP6, MARE1, T22D1, ELAV1, ELF2, NAB2, MYLK, TAB1, AAAT, MLF2, ITSN1, TBCC, VAS1, ZFHX3, ZYX, ETFD, SEPT7, ADRM1, UAP1, IBP7, AINX, LAMA4, EXT1, PSMD5, CSRP2, DDB1, CDC37, DPYL2, KCC4, RBBP7, TAF9, ECM1, SRSF7, CPSF6, DREB, NRF1, FSCN1, IF16, DECR, GLO2, H2A2C, NDUA9, PCKGM, DDR2, HCDH, UGPA, TRXR1, MIC60, CPEB4, HNRL2, INF2, RFX7, QSER1, AAK1, PRSR3, QRIC1, LRRF1, P3H1, MA7D1, AL1L2, K2C71, TIM50, FUT11, TB10B, ANO6, FIL1L, SVEP1, AMOT, EPC2, FND3B, CRTC2, QORX, DHB12, CYBR1, IN80D, PAN3, YIF1B, F133B, ZN326, FILA2, MEST, HERC4, PIGG, BCORL, FA76B, TGO1, PREP, PRC2B, RRP12, TOIP1, PCID2, EOGT, TTC38, TM201, NU188, HP1B3, CE170, ZN362, FBP1L, FKB15, ZEP3, ZC3HD, LRIF1, UBR4, STXB5, RHG21, RM02, UBAP2, KPRP, KPLCE, RBM26, WLS, TUT4, H37, NT5D1, AHDC1, MRCKA, RPRD2, MYOME, ZN318, BROX, TASO2, PEAR1, MBNL2, ZMYM4, FHI2A, CD276, TSH3, TENS2, KANK2, AR6P4, OLM2A, HGNAT, ARID2, TENS3, CRBG3, RHG17, BICRL, AMERL, ATLA3, NXN, IQEC1, VASN, CPIN1, PTRD1, ELP2, LTOR1, TWF2, ADNP2, K2C80, LIN54, SCMC1, TM214, PPR18, CAVN1, CDC73, RM14, TATD1, EDC4, PRP8, SCYL2, GOLM2, NFRKB, RL22L, ALKB5, NCEH1, MDEAS, ZC3HE, OGFD3, LARP1, C1TM, FIP1, CRTC1, CSPG4, ARAID, LRSM1, TMCO3, LCLT1, CREL2, PAMR1, FAT4, MCAF1, CP2R1, PACS1, BCOR, MPRIP, HACD2, GGYF2, HSDL2, KAT3, CERS6, THSD4, MEX3B, ZN574, RN111, BAKOR, SRCAP, RIPR1, YJ005, TSH1, BGIN, UBN2, TMTC3, RAPH1, MOB2, IKIP, H32, LARP4, TBA1A, RS27L, HAKAI, ASXL2, CCD80, SPT6H, SND1, DDX46, 5MP2, DHX30, EIF3M, CYFP1, TAOK1, KDM3B, PHF5A, ERMP1, ZCCHV, NUP54, POGZ, MON2, K1C27, NUFP2, MAVS, CLAP1, DHX29, PLGT3, LIMS2, HDGR2, DCXR, EMSY, RAI1, I2BP2, RBBP6, SH3R1, RABEK, HUWE1, YTHD3, K2C1B, KHDC4, TMED4, COXM1, CENPV, GALT5, PHLB2, GLT10, MYPN, SYVN1, ACOT1, PABP2, LDB1, LYRIC, ZN598, KTN1, BCL9L, PHLB1, LUZP1, GP180, CAND1, HOOK3, TSYL5, CARM1, PRSR1, MEX3D, DDX42, P66A, HORN, RB6I2, RELL1, PLD3, FOXP4, P3H2, P3H3, CCD50, SPA12, CTL2, WDFY1, TEX2, NXP20, MGAP, Z3H7A, CHERP, ANKH1, SUGP1, CCAR1, DJC10, MSRB3, PLPL6, MILK2, SPB1, SMAP1, P20D2, PHAR4, ZNF34, ELMD2, DCP1B, XRN1, MAML2, ABI1, SELH, SPART, RPTOR, CCAR2, SIX5, NUP93, K2C78, ZCH24, LTBP4, ASCC3, SYNPO, FNBP4, AFAP1, CERS5, NKAP, CPSF7, ARFG2, ARFG1, LRC17, EMC1, ENAH, RM43, YP023, ANR52, GT251, SUMF2, SUMF1, PGLT1, PCYXL, TXND5, SCPDL, SERB1, LEMD2, NECP1, FA98A, CHSTE, APCDL, RN214, LS14A, TNR6A, PHC3, ABCF1, SP20H, ZNT7, NAV1, VP37A, FBX22, PCAT1, ZMIZ2, ARI1B, NUP35, NEUA, PLBL2, MFSD8, NEDD1, ZNT5, G45IP, SMRC2, NPL4, PUM2, KISHA, RDH11, STT3B, SPP2B, HM13, ALMS1, NEK9, PKHO2, DDX54, DLG5, NEK7, GPX8, GEMI5, IPO4, ZN384, SETD7, F222B, SMAP2, CHUR, CEMIP, PDC6I, FBLI1, PHLA1, NUDC2, SCFD1, POF1B, LMO7, ATX2L, SELM, PALLD, SREK1, PSPC1, P66B, AUTS2, ZCH14, IRGQ, DDB2, ASM3A, DDX1, S39A7, FAM3C, GBF1, SMG7, RTF1, NICA, TM9S4, TM131, RT27, F168A, PHF3, MAML1, HS105, LAR4B, GCN1, ZN516, NU205, PXDN, AN32B, NECT2, TFG, ARC1A, STAM1, REQU, SC65, CBP, GGH, NELL1, DDX17, TANK, CELF1, GSLG1, RENT1, CSN5, GATA6, SMRC1, FUBP2, TNPO1, ARHG2, UBP13, USP9X, UBP7, LPP, RBPMS, SMCE1, CAVN3, MYDGF, YIPF5, PIGT, RL36L, ZN622, WBP2, NCLN, MRTFA, ERGI1, RFT1, FERM2, FUBP1, TTC17, LRC59, PBIP1, FKB10, AKTS1, PF21A, EFHD2, GALM, INT12, CTHR1, KLH29, OPTN, AP2M1, RCN3, REPS1, KBP, DAZP1, RBM33, CK024, ZN503, I17RA, OTUB1, PGM2, CERS2, ZC21A, P121A, PDLI5, CREL1, ERO1A, PGAM5, FUBP3, SUCB2, GMPPA, KIRR1, WNK4, TMX3, CHAP1, ZFP91, PDLI2, ZC3HA, CLP1L, SCYL1, Z512B, CNDP2, ZFR, B3GT6, EP400, VATG3, PRRC1, ZN512, NOL4L, MBOA7, DOCK7, TOX2, SPB12, ARHGH, RBM14, QKI, LENG8, GSDMA, PP1RA, S38A2, VPS35, PHF12, SNX18, CIC, MED15, ERGI2, NUDC1, ERBIN, PIGS, WRIP1, RANB9, CLCC1, UBL7, MYADM, SIN3A, RUFY1, MINT, MMS19, UHRF1, NIBA2, HTF4, TBCB, NELL2, PSB7, CNN2, SEC62, PCY2, K1C12, CDC5L, PSMD1, SDF2, PARK7, EYA3, NEUR1, VAT1, LGMN, PLIN2, NUP88, MNT, SCAFB, DNJC7, PHB2, RGPD5, PITX2, ATX2, HCD2, COCA1, SMAD5, ROAA, LITAF, NP1L4, ACON, TM9S2, TS101, CPNE1, TCPH, EBP2, ANM1, SH3G1, CND3, DDX50, MEP50, VKOR1, TBA1C, SELS, MBB1A, COR1B, TXD17, VPS25, RM45, MXRA8, CAB45, ADPGK, PELO, ERP44, LXN, ESYT1, CNPY3, LIMD2, CSN4, WAC, DIDO1, DCTN5, AASD1, TMM43, TBCD, TBB6, HNRL1, HTAI2, DDX23, DHRS6, CA050, WDR18, THUM3, RN126, TBB2B, TM109, TMED9, NUP58, ELOV1, THIC, REPI1, RBM4, SFXN3, SSBP3, NAA15, KLF16, SRRT, TGT, HDHD5, EIF2A, CADM1, MK67I, YTHD1, WNK3, NEUL, RM37, GTPB4, UACA, RAB34, TBL1R, UBL5, EDEM3, API5, K1C23, UNK, FTO, TB182, AMRA1, TTYH3, ADSSP, PITH1, SKI8, SLIRP, WWTR1, TWSG1, NAA50, MKRN2, PAIP1, LSG1, NAT10, XRN2, SP130, BRD8, DDX47, MAGT1, LMA2L, SIL1, I2BPL, NUCKS, EHD4, VPS16, SH3L3, EPC1, SLK, S38A1, PDCL3, RBGPR, ADNP, DPH5, HIPK2, FOXP1, CK068, BOLA2, TMX1, NELFA, GCP60, PTN23, UN45A, OFUT1, WNK1, AMPB, GAPR1, ZHX3, EHD1, ZN768, SG196, CC134, PEAK1, AAMDC, WDR26, PKHG2, ZN703, ACAD9, GORS2, JUPI2, SYP2L, SFXN1, FKRP, ELP3, KT3K, FBRS, MLXIP, PKHA5, GBB4, XPO5, GRPE1, MYG1, RC3H2, TENS1, TAF9B, EMAL4, GLOD4, ZBT20, NCOA5, TANC2, MOV10, ZN532, ZN160, TNR6C, CHD8, SDF2L, CD248, SEC12, S10AE, AT131, RM47, CHM1A, TM9S3, APMAP, TRXR2, ARFG3, RAB18, VTA1, CD320, UBN1, DCP1A, TF7L2, RTN4, NIT2, NECT3, EXOS3, ANLN, XPP1, GEPH, PDLI7, DDX21, SAR1A, SIAS, SHLB2, MBNL1, 4ET, AAAS, STRN4, UBQL4, HEBP1, ABC3C, PHP14, F1142, TM7S3, KRT84, SYFB, SYIM, BMP2K, ATG3, SMC4, SAC1, OLA1, ZF64B, RBM12, ABHDA, SHFL, T106B, SPS2L, DD19A, TBC23, CC50A, SEP11, MED17, DJC11, INT7, ATD3A, ARL8B, DDX18, RT18A, NLE1, ZN358, RBM22, ARGL1, RM22, CZIB, GEMI8, F120C, OCAD1, IMPA3, MIC19, CKLF6, P4HTM, TOR4A, TRM1, CARF, DPP3, DDX56, BCLF1, TAB2, M3K20, UGGG2, UGGG1, CDK12, TECR, ERAP1, GGA3, F120A, GDE1, IF2B1, MAT2B, MYOF, ITSN2, BICRA, EHD2, CNOT2, CALL5, CRIM1, HACD3, KCMF1, RAI14, RM27, SENP1, SH3B4, PHRF1, RCC2, SLAI2, TEN3, CT2NL, RRBP1, SYLC, RBM27, KANL3, ANFY1, RERE, SUCB1, LRIT1, DPM3, SAE1, COPG2, MRC2, GBG12, DHCR7, DKK3, VPS29, EIF3K, GRHPR, CATZ, SAE2, NXF1, B4GT7, PEF1, FBLN5, CLIP2, ZO2, DNJB4, ADDG, ABCF2, TES, LIMD1, Z3H7B, TCF20, SUN2, LIMA1, SRP68, CHRD1, SEPT9, UBQL2, PCYOX, DDX20, ATS1, DPP2, CEIP2, NB5R1, S30BP, MED13, PUF60, NRBP, VATH, CBPA4, XPO7, BAZ2B, SIX4, GGT7, MSRA, NAGK, DBNL, DCTN4, CDC23, STML2, DBR1, AKA11, GMEB2, CPSF3, PARP4, RALY, ITA11, NUP50, ZHX1, ZN346, DNPEP, MCTS1, S39AA, ASAP1, MRTFB, HEG1, ZMIZ1, PRR12, YETS2, HECD1, ZMYD8, COR1C, NOTC3, SPAT2, PPT2, PRP19, UBQL1, SNX12, SYNRG, G3BP2, CHIP, PACN2, MAGD2, SNX6, PSD13, FAF1, PPIE, CSN3, MINP1, S12A4, MACF1, SCAF8, TRI33, TNR6B, SMAG1, CE164, FOXJ3, SHAN2, COR2B, SRRM2, PA2G4, ZN148, RTRAF, RUVB2, CLC11, EIF3L, PLAP, RUVB1, NUDC, VDAC3, COF2, ERGI3, SYFA, DRG1, NCKP1, PLAK2, ZN652, MA2B2, OFUT2, FND3A, E41L3, R3HD2, RRP44, LRCH1, GSTK1, DDX52, RT07, TMA7, MAN1, CHSP1, TR150, NOP58, ZN281, SGT1, ACOT9, NOSIP, MEMO1, SHLB1, LC7L2, SBDS, TMED7, ORN, UFC1, STRAP, RTCB, ZN330, RL36, SAMH1, TLN1, ARIP4, MTCL1, TCAF1, UBP15, LOXL2, CRBG1, HYOU1, TBL2, KLF12, ARI1, LSM4, RN114, PRC2C, RBM7, YTHD2, SP16H, SRPRB, MRCKB, ZN706, MAGD1, SNX5, HCFC2, FHOD1, SERC, NCOR2, NPTN, CBPQ, SOX21, RT18B, COPG1, FKBP7, GMEB1, CLIC4, EMIL1, MTCH2, 5MP1, DC1L1, EPN1, NEMO, IF2B2, ZNT1, NCOA3, NUMBL, PIAS3, ZHX2, S23IP
Species: Bos taurus, Homo sapiens
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Hou C, Wu C, Wu Z, Cheng Y, Li W, Sun H, Ma J. Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics. Journal of proteome research 2024 39302247
Abstract:
O-Linked β-N-acetylglucosamine (O-GlcNAc) modification (i.e., O-GlcNAcylation) on proteins plays critical roles in the regulation of diverse biological processes. However, protein O-GlcNAcylation analysis, especially at a large scale, has been a challenge. So far, a number of enrichment materials and methods have been developed for site-specific O-GlcNAc proteomics in different biological settings. Despite the presence of multiple methods, their performance for the O-GlcNAc proteomics is largely unclear. In this work, by using the lysates of PANC-1 cells (a pancreatic cancer cell line), we provided a head-to-head comparison of three affinity enrichment methods and materials (i.e., antibody, lectin AANL6, and an OGA mutant) for site-specific O-GlcNAc proteomics. The enriched peptides were analyzed by HCD product-dependent EThcD (i.e., HCD-pd-EThcD) mass spectrometry. The resulting data files were processed by three different data analysis packages (i.e., Sequest HT, Byonic, and FragPipe). Our data suggest that each method captures a subpopulation of the O-GlcNAc proteins. Besides the enrichment methods, we also observe complementarity between the different data analysis tools. Thus, combining different approaches holds promise for enhanced coverage of O-GlcNAc proteomics.
O-GlcNAc proteins:
NBAS, SBNO1, PRS37, CNOT1, MGT4D, P121C, P20L1, MCRI1, SPT5H, MANBA, AGRIN, BCL9, NOP56, ARI1A, ABLM1, KMT2D, SCAM3, MYPT1, HNRDL, XPO1, SYN3, SC16A, SYNJ2, SYNEM, TIF1A, LAMA5, MCES, DC1L2, CP110, IF4G3, E41L2, ZN207, BUB1, HTSF1, AKAP8, DHX16, MGRN1, TRAK2, KIF1B, PLIN3, MAFK, IF2P, DTNB, MITF, SRGP2, ATG13, ZC11A, PP6R2, ANR17, LRP5, NDUS2, NCOR1, U520, UTP20, WDHD1, FACE1, TOX4, SC24D, SUN1, SC31A, CE152, UBR5, AGFG2, APOL3, IPO7, SVIL, SC24A, SC24B, ZMYM6, GPR75, LATS1, LMNA, GCR, OAT, CPNS1, HSPB1, GNAI2, A4, K1C18, ATPB, SAP, PROF1, HS90A, HS90B, NFIC, VIME, SNRPA, ATX1L, DERPC, PTPRF, ESTD, ODPB, C1TC, SKIL, XRCC6, CCNB1, ATF2, NDKA, GNS, ZEP1, AT2A2, ATF7, ERCC2, EGR1, ATF1, GGT1, AT2B1, FLNA, 5NTD, PUR2, RFX1, SFPQ, RS3, STOM, ARNT, MAP4, KPYR, CLIP1, HXC9, ZEP2, QCR1, I5P2, ELF1, MRP1, TRY3, CAH8, T2FA, NU214, NUP62, STAT3, ECHA, HNF4A, LAP2A, LAP2B, CACP, GATA4, BAG6, MAP1B, STT3A, RFX5, PAXI, LMAN1, CDK8, CENPF, YLPM1, NU153, RBP2, GSK3A, TAF6, DNLI3, EMD, TCPD, PAPOA, HNRPM, AGFG1, STAT2, NUP98, ATX1, ATN1, RD23B, AF10, BRPF1, NP1L1, EIF3B, MAZ, HDAC4, IF6, H2B1D, ACTB, ABCE1, RRAS2, ERF1, RL32, ACTG, EF1A1, CSK21, F193A, SARNP, FOXK1, ZBED6, RHG04, CLH1, SPTB2, TIAR, SP2, DYST, ATP7A, NOTC2, TLE4, PTN12, FAK1, ZO1, ACK1, DHX9, EP300, AHNK, NEXN, CPSF1, WASC5, TROAP, BPTF, SF3A3, TP53B, PTN13, TRAP1, DLG1, ATM, PPIL2, TCOF, SMAD4, PICAL, MAMD1, ASPP2, RIN1, CDK13, VEZF1, UBP2L, SRC8, CAPR1, ITPR1, MDC1, RRP1B, UBP10, COG2, MEF2D, LASP1, IMB1, PLEC, NONO, SF3A1, JHD2C, ELF2, TAB1, NCOA1, ZYX, UAP1, DREB, PDS5A, QSER1, TXIP1, FHOD3, P3H1, EMAL3, ZN791, CHD9, TB10B, FND3B, CRTC2, BCORL, BRD10, CE170, ZN362, ZEP3, UBR4, UBAP2, AHDC1, RPRD2, ZN318, TUT7, RN213, TENS2, WAC2A, MAP1S, ARID2, TENS3, ANR40, BICRL, ATLA3, CPIN1, GRAM4, NIPBL, LIN54, RINT1, L2GL2, C2D1A, SCYL2, NFRKB, ZC3HE, LARP1, ZNT9, CRTC3, GLB1L, MCAF1, SRCAP, CFA65, UBN2, VP13C, RAPH1, H32, TMUB2, MARK2, DDX46, EIF3M, KDM3B, GRIN1, KANL1, POGZ, NUFP2, MAVS, DHX29, EMSY, RAI1, I2BP2, HUWE1, YTHD3, KAISO, MYPN, LYRIC, KTN1, PRSR1, DDX42, P66A, RHPN2, NUDC3, AHNK2, GID4, ARI3B, MA7D3, MGAP, LMTK2, ANKH1, SUGP1, MILK2, SRRM1, PHAR4, DCP1B, PELP1, TENS4, CCAR2, HROB, TXND5, RB15B, TNR6A, PHC3, NAV1, VP37A, SYNE1, FAD1, NUP35, TOIP2, KNL1, O52N2, TRY6, COP1, GOGA5, ALMS1, DLG5, MORC4, GEMI5, PIGO, PARD3, IPO4, TM263, PDC6I, LMO7, ATX2L, PHIP, P66B, BBX, SMG7, F168A, PRCC, RYR2, US6NL, SYMPK, RENT1, PF21A, EFHD2, KBP, F120B, RBM33, THOC1, P121A, PDLI5, VPS50, DNJC1, Z512B, ZFR, EP400, SENP8, PRRC1, DOCK7, RBM14, NEK1, PP1RA, PHF12, SPAG5, CIC, ERBIN, SIN3A, MINT, HTF4, VAT1, PLIN2, DNJC2, MNT, KIF2C, ATX2, ARI3A, GDF15, WAC, DIDO1, RFIP5, SRRT, SETD2, ABCA2, TRIM5, TANC1, ZN407, SP130, PUS7L, I2BPL, NELFA, CHM4B, WNK1, ZHX3, CDCP1, Z385D, BCAS3, PEAK1, ECT2, JUPI2, ZN408, PKHA1, ILRL2, RC3H2, TAF9B, NCOA5, TANC2, SYTL2, CHD8, UBN1, DCP1A, SEM4B, HPS4, PDLI7, 4ET, CHRC1, F1142, LTBP3, SYIM, IGSF5, RBM12, STAU2, TYDP1, SLTM, CARF, HXC10, TAB2, CDK12, ERAP1, MYOF, BICRA, CNOT2, SPN90, F135A, RBM27, KANL3, ZMYM2, LIMD1, TCF20, UBQL2, S30BP, PUF60, SIX4, TRM6, NOCT, TASOR, GMEB2, ACINU, CNO11, ASAP1, YETS2, ZMYD8, MYO6, SPAT2, PRP19, NSF1C, MACF1, TRAK1, SRRM2, SCML2, PDE10, AP3M1, ZN281, ZN711, TLN1, ARIP4, DCAF1, WAC2C, RPGF2, CRBG1, PRC2C, UTP18, SNX9, NCOR2, BIG1, NCOA3, PCLO, S23IP
Species: Homo sapiens
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Xiong Y, Lu Z, Shao Y, Meng P, Wang G, Zhou X, Yao J, Bao H, Lu H. Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation. National science review 2024 11(11) 39534244
Abstract:
Protein glycosylation, the most universal post-translational modification, is thought to play a crucial role in regulating multiple essential cellular processes. However, the low abundance of glycoproteins and the heterogeneity of glycans complicate their comprehensive analysis. Here, we develop a rapid and large-scale glycopeptide enrichment strategy via bioorthogonal ligation and trypsin cleavage. The enrichment process is performed in one tube to minimize sample loss and time costs. This method combines convenience and practicality, identifying over 900 O-GlcNAc sites from a 500 μg sample. Surprisingly, it allows simultaneous identification of N-glycosites, O-GlcNAc sites, O-GalNAc sites and N-glycans via a two-step enzymatic release strategy. Combined with quantitative analysis, it reveals the distinct O-GlcNAcylation patterns in different compartments during oxidative stress. In summary, our study offers a convenient and robust tool for glycoproteome and glycome profiling, facilitating in-depth analysis to elucidate the biological functions of glycosylation.
O-GlcNAc proteins:
MEIOC, SBNO1, CNOT1, HMX3, RGPD3, P121C, TAF4, ARI1A, CDKA1, ABLM1, KMT2D, RGPD8, MYPT1, SC16A, SET1A, TIF1A, NUP42, SYNJ1, ZN207, AKAP8, ZC3H1, GANP, DIAP1, MAFK, BRD4, MITF, T22D2, ANR17, NCOR1, CCNK, PIAS1, TOX4, ST65G, PCF11, NFAT5, SC31A, SVIL, SC24A, SC24B, CNOT4, EGFR, LMNA, HSPB1, RPN1, RPN2, RLA2, RLA0, AP2A, K1C18, K2C8, NPM, VIME, K2C7, SNRPA, ATX1L, TPR, GLU2B, PO2F1, ZEP1, JUNB, JUND, ATF7, DDX5, SON, ATF1, CSRP1, SFPQ, BRD2, ARNT, MAP4, CALX, PSB4, TEAD1, HXA11, HXC9, ELF1, NU214, NUP62, CUX1, MATR3, SSRA, SSRB, UTRN, STT3A, NEST, LMAN1, CDK8, YLPM1, NU153, RBP2, TAF6, EMD, DYN2, SMCA4, AGFG1, HNRPF, NUP98, ATN1, RD23B, AF10, AF17, FOXA1, CTBP2, RS16, NOMO3, PHC1, RAE1L, SARNP, FOXK1, HNRPU, SPTB2, FOXK2, TFAP4, KMT2A, IF4G1, GABPA, ZO1, EP300, BPTF, NFIA, FOXC1, ROA0, G3BP1, PICAL, MOGS, RUNX3, KLF5, CDK13, VEZF1, UBP2L, ELOA1, CAPR1, PUM1, RRP1B, NCOA6, GSE1, MEF2D, LASP1, ARI5B, ZN638, NUMA1, DAZP2, KIF14, EBP, PLEC, PCM1, PUM3, RBMS2, TEAD4, SF01, MED1, JHD2C, ELAV1, ELF2, TAB1, ZFHX3, ZYX, CCDC6, TAF9, IF16, RFX7, QSER1, CHD9, CRTC2, BCORL, BRD10, NOMO2, TGO1, PRC2B, ZN362, LRIF1, RHG21, UBAP2, AHDC1, RPRD2, ZN318, ZMYM4, ARID2, BICRL, NIPBL, LIN54, Z280D, MFSD5, SCYL2, NFRKB, RSBNL, GLD2, MDEAS, ZC3HE, CRTC3, SAS6, MCAF1, BCOR, GGYF2, CO039, SRCAP, UBN2, TMTC3, RAPH1, UBP54, SPT6H, KDM3B, POGZ, NUFP2, EMSY, RAI1, I2BP2, RBBP6, SH3R1, YTHD3, BCL9L, TIKI1, PRSR1, DDX42, P66A, RB6I2, AHNK2, GID4, TEX2, MGAP, ANKH1, SUGP1, SPB1, ZN687, SYNPO, FNBP4, MACOI, ARFG1, S43A3, LS14A, TNR6A, PHC3, KMT2C, KNL1, CHD6, PO210, PARD3, LMO7, P66B, BBX, ELYS, ZCH14, SMG7, ZN592, PRCC, US6NL, RREB1, CBP, HXB13, GPKOW, FUBP2, LPP, S2546, TOM6, PF21A, INT12, SNR40, RBM33, P121A, PDLI5, FUBP3, CHAP1, ZC3HA, Z512B, ZFR, EP400, NOL4L, RBM14, QKI, LENG8, CIC, STRBP, SIN3A, MINT, HTF4, MNT, SCAFB, TEAD3, ATX2, ARI3A, RBM4B, CNPY3, WAC, DIDO1, RBM4, YTHD1, AMRA1, SP130, BRD8, I2BPL, ADNP, FOXP1, E41L1, PEAK1, ECT2, FBRS, PKHA5, RC3H2, TAF9B, ZBT20, NCOA5, TANC2, CHD8, UBN1, PDLI7, 4ET, FANCI, NSMA3, CARF, CDK12, CNOT2, CHD7, RBM27, KANL3, RERE, TCF20, DPP2, GT2D1, PUF60, SIX4, CDC23, TASOR, GMEB2, ZHX1, ZBT21, PRR12, YETS2, PRP19, SCAF8, TRI33, SRRM2, SCML2, ZN148, HPSE, ZN281, FBX7, ARIP4, KDM3A, PLXD1, CRBG1, HYOU1, PRC2C, YTHD2, SRPRB, NCOR2, S23IP
Species: Homo sapiens
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Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X. Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells. Nature communications 2019 10(1) 31492838
Abstract:
Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per-O-acetylated, which, however, can induce a long-overlooked side reaction, non-enzymatic S-glycosylation. Herein, we develop 1,3-di-esterified N-azidoacetylgalactosamine (GalNAz) as next-generation chemical reporters for metabolic glycan labeling. Both 1,3-di-O-acetylated GalNAz (1,3-Ac2GalNAz) and 1,3-di-O-propionylated GalNAz (1,3-Pr2GalNAz) exhibit high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying 1,3-Pr2GalNAz in mouse embryonic stem cells (mESCs), we identify ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We show that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase at serine 25, which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.
O-GlcNAc proteins:
A0A087X1C1, A0A0B4J203, A0A0C4DFX4, SRCRL, SBNO1, CNOT1, IQCAL, RGPD3, LRIQ3, P121C, YU005, H0YHG0, H3BMQ9, H8Y6P7, I3L521, PDLI1, TAF4, P3C2A, DDX3X, NFIB, ARI1A, ABLM1, KMT2D, ZN197, RGPD8, MYPT1, ZN609, ZN646, SET1A, SYNEM, ZN185, NUP42, SI1L1, TGFI1, VIP2, M3K7, TPD54, SYNJ1, IF4G3, WIPF1, SMAD6, MYPT2, PLIN3, MAFK, N4BP1, ANR17, NCOR1, GGYF1, PRDM1, STAM2, TOX4, AGFG2, UNC5C, VENTX, SC24B, PCNT, ZBT11, CNOT4, BAG3, TXD12, TTLL1, APCL, NSD2, EGFR, IGF2, CRYAB, LMNA, ALDOA, GCR, HSPB1, PCCA, RLA2, JUN, HEP2, K1C18, ANXA2, ADRB2, NFIC, VIME, 5HT1A, SNRPA, ROA1, CO4B, ATX1L, FMAS1, GRL1A, DERPC, C1C1L, GLI2, TPR, GYS1, MYL6B, PO2F1, ATF2, ZEP1, RS2, ITB4, JUNB, JUND, ATF7, SON, ATF1, NEBU, CSRP1, NF1, ROA2, RFX1, CBL, COF1, IF4B, ARNT, MAP4, CALX, TEAD1, PDIA3, CDC27, CLIP1, ZEP2, ELF1, TTK, PCKGC, ADDA, NU214, MP2K2, NUP62, VKGC, VATA, CUX1, TXLNA, PBX2, HELZ, UTRN, RFX5, PAXI, NR2C2, NASP, CENPF, YLPM1, NU153, RBP2, TAF6, EMD, PAPOA, AGFG1, NUP98, ATX1, MYOM2, AF10, AF17, DSRAD, NU107, RL8, F193A, PITX1, PHC1, KGD4, SARNP, FOXK1, HTD2, DAB2, RHG04, VIGLN, HNRPU, SPTB2, SCN7A, FOXK2, EWS, MEF2A, SP2, NUCB1, IF4G1, NOTC2, TLE4, NMDZ1, GABPA, ZO1, ACK1, CACB2, EP300, AHNK, MGAT2, GALT2, FOXO1, SNF5, BPTF, NFIA, DPYD, TP53B, ZN155, FOXC1, AKAP6, ROA0, GPS2, G3BP1, KCAB2, PABP4, PLD1, PICAL, MAMD1, RIPK1, SNW1, MTMR1, CUL4B, ASPP2, NFYC, CDK13, TOB2, DAG1, VEZF1, DSG2, UBP2L, GIT2, SRC8, MDC1, EPN4, RRP1B, NCOA6, GSE1, MEF2D, ARI5B, NUMA1, PSME4, SART3, KIF14, BRD3, EBP, PLEC, RBMS2, TAF1C, SF01, MED1, JHD2C, MARE1, ELF2, TAB1, ZFHX3, ZYX, ADRM1, TAF9, RFX7, QSER1, QRIC1, ZN800, LR75B, EPC2, CRTC2, YIF1B, ZN326, BRD10, PRC2B, SYAM, CE170, NHSL1, ZN362, ZEP3, LRIF1, UBR4, SKT, RHG21, UBAP2, RBM26, RC3H1, VP13D, RPRD2, ZN318, TASO2, TTC23, ERR2, KAZRN, ARID2, RHG17, ANR40, BICRL, NIPBL, LIN54, NFRKB, ZN449, RSBNL, MDEAS, ZC3HE, CRTC3, SAS6, MCAF1, BCOR, MPRIP, GGYF2, BNC2, FGD5, CO039, SRCAP, YJ005, UBN2, RAPH1, UBP54, PREX2, HAKAI, ASXL2, SPT6H, KDM3B, ZCCHV, RGPD4, POGZ, SZRD1, MAVS, EMSY, RAI1, I2BP2, SRGP1, SH3R1, YTHD3, STRA8, MYPN, TLK2, ZFHX4, BCL9L, IQCH, SNX32, PRSR1, MEX3D, DDX42, CACL1, P66A, CC125, KCC1D, HID1, AHNK2, FOXP4, NAV2, MGAP, RP1L1, PHF6, ANKH1, SUGP1, CCAR1, RPAP2, MILK2, EFC13, PHAR4, XRN1, TBC3A, TENS4, SPART, NUP93, ZN687, SYNPO, FNBP4, TAB3, CPSF7, ARFG1, ENAH, XXLT1, CHSTE, TNR6A, PHC3, SP20H, NAV1, VP37A, KMT2C, ARI1B, NUP35, TDRD7, NEDD1, PUM2, ALMS1, DLG5, ZN384, WIPF2, FRS2, F222B, SMAP2, IASPP, ZFN2B, TWST2, PCNP, LMO7, ATX2L, STAB2, PALLD, CSKI2, SRS12, P66B, BBX, SMG7, RTF1, PHF3, MAML1, LAR4B, PRP16, PRCC, CBP, EVPL, DDX17, GPKOW, FUBP2, LPP, FUBP1, TTC28, PF21A, KLH29, RBM33, MMAB, EF2KT, GWL, P121A, PDLI5, INT4, FUBP3, PAWR, ANCHR, Z512B, ZFR, EP400, COG8, RBM14, QKI, LENG8, CIC, MED15, ERBIN, MINT, HTF4, TEAD3, RGPD5, CGRE1, ATX2, CTIP, SH3G1, DPH2, WAC, DIDO1, TBCD, HNRL1, HIRP3, CAR11, YTHD1, GTPB4, AMRA1, TANC1, CEP44, MFF, SP130, BRD8, RGAP1, I2BPL, RBNS5, ADNP, FOXP1, PTN23, CA198, WNK1, E41L1, ZHX3, ILRUN, PEAK1, PKHG2, ECT2, JUPI2, PKHA5, RC3H2, TAF9B, ZBT20, NCOA5, TANC2, ZN532, ARFG3, PLPL8, UBN1, PCD12, INCE, PDLI7, 4ET, DIAP3, PDS5B, RBM12, CCD87, CARF, TAB2, MS18A, CDK12, ITSN2, WHRN, DAPLE, SLAI2, BAHC1, BCCIP, C2D2A, RBM27, KANL3, ZN219, LIMD1, TCF20, UBQL2, S30BP, NRBP, CTNA3, BAZ2B, HERC5, SIX4, TASOR, GMEB2, PARP4, NUP50, ZHX1, MRTFB, PRR12, YETS2, HECD1, SPAT2, SCAF8, LIMC1, ZC3H4, SRRM2, SCML2, ZN148, ZFP30, WDR37, MYH15, R3HD2, ZN281, COQ6, DCAF1, RPGF2, CRBG1, PRC2C, RBM7, CD2AP, TSSC4, HCFC2, NCOR2, GMEB1, DC1L1, NCOA3, ZHX2, S23IP, U3KPZ7
Species: Mus musculus, Homo sapiens
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