References
- Spiro RG. Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology. 2002;12(4):43R–56R. doi: 10.1093/glycob/12.4.43R
- Synthesis BE. Processing, and function of N-glycans in N-glycoproteins. Adv Neurobiol. 2014;9:47–70.
- Jensen PH, Kolarich D, Packer NH. Mucin-type O-glycosylation–putting the pieces together. FEBS J. 2010;277(1):81–94. doi: 10.1111/j.1742-4658.2009.07429.x
- Cheng XG, Cole RN, Zaia J, et al. Alternative O-glycosylation/O-phosphorylation of the murine estrogen receptor beta. Biochemistry. 2000;39(38):11609–11620. doi: 10.1021/bi000755i
- Xu S, Tong M, Suttapitugsakul S, et al. Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins. Cell Rep. 2022;39(11):110946. doi: 10.1016/j.celrep.2022.110946
- Sun F, Suttapitugsakul S, Wu R. Enzymatic tagging of glycoproteins on the cell surface for their global and site-specific analysis with mass spectrometry. Anal Chem. 2019;91(6):4195–4203. doi: 10.1021/acs.analchem.9b00441
- Xiao HP, Suttapitugsakul S, Sun FX, et al. Mass spectrometry-based chemical and enzymatic methods for global analysis of protein glycosylation. Acc Chem Res. 2018;51(8):1796–1806. doi: 10.1021/acs.accounts.8b00200
- Riley NM, Bertozzi CR, Pitteri SJ. A pragmatic guide to enrichment strategies for mass spectrometry-based glycoproteomics. Mol & Cell Proteomics. 2021;20:100029. doi: 10.1074/mcp.R120.002277
- Suttapitugsakul S, Sun F, Wu R. Recent advances in glycoproteomic analysis by mass spectrometry. Anal Chem. 2020;92(1):267–291. doi:10.1021/acs.analchem.9b04651
- Sun FX, Suttapitugsakul S, Wu RH. Systematic characterization of extracellular glycoproteins using mass spectrometry. Mass Spectrom Rev. 2023;42(2):519–545. doi:10.1002/mas.21708
- Xiao H, Chen W, Smeekens JM, et al. An enrichment method based on synergistic and reversible covalent interactions for large-scale analysis of glycoproteins. Nat Commun. 2018;9(1):1692. doi:10.1038/s41467-018-04081-3
- Yang WM, Ao MH, Hu YW, et al. Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO). Mol Syst Biol. 2018;14(11):e8486. doi: 10.15252/msb.20188486
- Xu S, Yin K, Wu R. Combining selective enrichment and a boosting approach to globally and site-specifically characterize protein co-translational O-GlcNAcylation. Anal Chem. 2023;95(9):4371–4380. doi:10.1021/acs.analchem.2c04779
- Chen WX, Smeekens JM, Wu RH. Systematic and site-specific analysis of N-sialoglycosylated proteins on the cell surface by integrating click chemistry and MS-based proteomics. Chem Sci. 2015;6(8):4681–4689. doi:10.1039/C5SC01124H
- Xiao H, Wu R. Quantitative investigation of human cell surface N-glycoprotein dynamics. Chem Sci. 2017;8(1):268–277. doi:10.1039/C6SC01814A
- Suttapitugsakul S, Tong M, Wu RH. Time-resolved and comprehensive analysis of surface glycoproteins reveals distinct responses of monocytes and macrophages to bacterial infection. Angew Chem Int Ed. 2021;60(20):11494–11503. doi:10.1002/anie.202102692
- Sun SS, Hu YW, Ao MH, et al. N-Glycositeatlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. Clin Proteomics. 2019;16(1):35. doi: 10.1186/s12014-019-9254-0
- Huang J, Wu M, Zhang Y, et al. OGP: a repository of experimentally characterized O-glycoproteins to facilitate studies on O-glycosylation. Int J Genomics Proteomics. 2021;19(4):611–618. doi: 10.1016/j.gpb.2020.05.003
- Hornbeck PV, Zhang B, Murray B, et al. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015;43(D1):D512–D520. doi:10.1093/nar/gku1267
- Ma JF, Li YX, Hou CY, et al. O-GlcNAcAtlas: a database of experimentally identified O-GlcNAc sites and proteins. Glycobiology. 2021;31(7):719–723. doi:10.1093/glycob/cwab003
- Kuster B, Mann M. 18O-labeling of N-glycosylation sites to improve the identification of gel-separated glycoproteins using peptide mass mapping and database searching. Anal Chem. 1999;71(7):1431–1440. doi:10.1021/ac981012u
- Suttapitugsakul S, Ulmer LD, Jiang C, et al. Surface glycoproteomic analysis reveals that both unique and differential expression of surface glycoproteins determine the cell type. Anal Chem. 2019;91(10):6934–6942. doi:10.1021/acs.analchem.9b01447
- Chen W, Smeekens JM, Wu R. A universal chemical enrichment method for mapping the yeast N-glycoproteome by mass spectrometry (MS). Mol & Cell Proteomics. 2014;13(6):1563–1572. doi: 10.1074/mcp.M113.036251
- Pearce OMT, Laubli H. Sialic acids in cancer biology and immunity. Glycobiology. 2016;26(2):111–128. doi: 10.1093/glycob/cwv097
- Riley NM, Malaker SA, Driessen MD, et al. Optimal dissociation methods differ for N- and O-glycopeptides. J Proteome Res. 2020;19(8):3286–3301. doi: 10.1021/acs.jproteome.0c00218
- Zeng WF, Cao WQ, Liu MQ, et al. Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3. Nat Methods. 2021;18(12):1515–1523. doi: 10.1038/s41592-021-01306-0
- Polasky DA, Yu FC, Teo GC, et al. Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods. 2020;17(11):1125–1132. doi: 10.1038/s41592-020-0967-9
- Fang P, Ji Y, Silbern I, et al. Evaluation and optimization of high-field asymmetric waveform ion-mobility spectrometry for multiplexed quantitative site-specific N-glycoproteomics. Anal Chem. 2021;93(25):8846–8855. doi: 10.1021/acs.analchem.1c00802
- Reiding KR, Bondt A, Franc V, et al. The benefits of hybrid fragmentation methods for glycoproteomics. TRAC-Trends Anal Chem. 2018;108:260–268. doi: 10.1016/j.trac.2018.09.007
- Steentoft C, Vakhrushev SY, Vester-Christensen MB, et al. Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines. Nat Methods. 2011;8(11):977–982. doi: 10.1038/nmeth.1731
- Lu L, Riley NM, Shortreed MR, et al. O-Pair search with MetaMorpheus for O-glycopeptide characterization. Nat Methods. 2020;17(11):1133–1138. doi: 10.1038/s41592-020-00985-5
- Malaker SA, Pedram K, Ferracane MJ, et al. The mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins. Proc Natl Acad Sci U S A. 2019;116(15):7278–7287. doi: 10.1073/pnas.1813020116
- Smeekens JM, Xiao H, Wu R. Global analysis of secreted proteins and glycoproteins in Saccharomyces cerevisiae. J Proteome Res. 2017;16(2):1039–1049. doi: 10.1021/acs.jproteome.6b00953
- Nie S, Lo A, Wu J, et al. Glycoprotein biomarker panel for pancreatic cancer discovered by quantitative proteomics analysis. J Proteome Res. 2014;13(4):1873–1884. doi: 10.1021/pr400967x