OGP: A Repository of Experimentally Characterized O-glycoproteins to Facilitate Studies on O-glycosylation

Hudson, 2017, Glycosylation precursors, 293 Boskovski, 2013, The heterotaxy gene GALNT11 glycosylates Notch to orchestrate cilia type and laterality, Nature, 504, 456, 10.1038/nature12723 Wolfert, 2013, Adaptive immune activation: glycosylation does matter, Nat Chem Biol, 9, 776, 10.1038/nchembio.1403 Campos, 2015, Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery, Mol Cell Proteomics, 14, 1616, 10.1074/mcp.M114.046862 Steentoft, 2011, Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines, Nat Methods, 8, 977, 10.1038/nmeth.1731 Ali, 2014, The O-glycomap of lubricin, a novel mucin responsible for joint lubrication, identified by site-specific glycopeptide analysis, Mol Cell Proteomics, 13, 3396, 10.1074/mcp.M114.040865 Yang, 2018, Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO), Mol Syst Biol, 14, 10.15252/msb.20188486 Zhang, 2018, Systems analysis of singly and multiply O-glycosylated peptides in the human serum glycoproteome via EThcD and HCD mass spectrometry, J Proteomics, 170, 14, 10.1016/j.jprot.2017.09.014 Zhao, 2020, An integrated mass spectroscopy data processing strategy for fast identification, in-depth, and reproducible quantification of protein O-glycosylation in a large cohort of human urine samples, Anal Chem, 92, 690, 10.1021/acs.analchem.9b02228 Mao, 2019, A new searching strategy for the identification of O-linked glycopeptides, Anal Chem, 91, 3852, 10.1021/acs.analchem.8b04184 Qin, 2017, Proteomics analysis of O-GalNAc glycosylation in human serum by an integrated strategy, Anal Chem, 89, 1469, 10.1021/acs.analchem.6b02887 Cao, 2021, Recent advances in software tools for more generic and precise intact glycopeptide analysis, Mol Cell Proteomics, 20, 10.1074/mcp.R120.002090 Cao, 2020, Novel methods in glycomics: a 2019 update, Expert Rev Proteomics, 17, 11, 10.1080/14789450.2020.1708199 Huang, 2020, Development of a computational tool for automated interpretation of intact O-glycopeptide tandem mass spectra from single proteins, Anal Chem, 92, 6777, 10.1021/acs.analchem.0c01091 Gupta, 1999, O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins, Nucleic Acids Res, 27, 370, 10.1093/nar/27.1.370 Campbell, 2014, UniCarbKB: building a knowledge platform for glycoproteomics, Nucleic Acids Res, 42, D215, 10.1093/nar/gkt1128 Malik, 2010, PROCARB: a database of known and modelled carbohydrate-binding protein structures with sequence-based prediction tools, Adv Bioinformatics, 2010, 10.1155/2010/436036 Huang, 2016, dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins, Nucleic Acids Res, 44, D435, 10.1093/nar/gkv1240 Huang, 2019, dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications, Nucleic Acids Res, 47, D298, 10.1093/nar/gky1074 Bhat, 2012, ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins, Nucleic Acids Res, 40, D388, 10.1093/nar/gkr911 Cooper, 2001, GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources, Nucleic Acids Res, 29, 332, 10.1093/nar/29.1.332 Cooper, 2003, GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources update, Nucleic Acids Res, 2003, 511, 10.1093/nar/gkg099 Kao, 2015, A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs, BMC Bioinf, 16, S10, 10.1186/1471-2105-16-S18-S10 Kawasaki, 2006, GlycoEpitope: the integrated database of carbohydrate antigens and antibodies, Trends Glycosci Glycotechnol, 18, 267, 10.4052/tigg.18.267 Baycin-Hizal, 2011, GlycoFly: a database of Drosophila N-linked glycoproteins identified using SPEG–MS techniques, J Proteome Res, 10, 2777, 10.1021/pr200004t Zhang, 2006, UniPep–a database for human N-linked glycosites: a resource for biomarker discovery, Genome Biol, 7, R73, 10.1186/gb-2006-7-8-r73 Kaji, 2003, Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins, Nat Biotechnol, 21, 667, 10.1038/nbt829 Kaji, 2006, Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site–specific stable isotope tagging, Nat Protoc, 1, 3019, 10.1038/nprot.2006.444 Zhou, 2012, A novel model to predict O-glycosylation sites using a highly unbalanced dataset, Glycoconj J, 29, 551, 10.1007/s10719-012-9434-x Steentoft, 2013, Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology, EMBO J, 32, 1478, 10.1038/emboj.2013.79 Audagnotto, 2017, Protein post-translational modifications: in silico prediction tools and molecular modeling, Comput Struct Biotechnol J, 15, 307, 10.1016/j.csbj.2017.03.004 de Las, 2019, Polypeptide GalNAc-Ts: from redundancy to specificity, Curr Opin Struct Biol, 56, 87, 10.1016/j.sbi.2018.12.007