{"doi":"10.1101/2023.06.13.541482","title":"Functional glycoproteomics by integrated network assembly and partitioning","abstract":"SUMMARY The post-translational modification (PTM) of proteins by O-linked β- N -acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describe N etworking of I nteractors and S ubstrat E s (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":391389,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9457,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1150477,"name":"John W. Thompson","orcid":null,"position":1,"is_corresponding":false},{"id":1164115,"name":"Yao Xiao","orcid":"0009-0002-4420-7153","position":2,"is_corresponding":false},{"id":289198,"name":"Michael J. Sweredoski","orcid":"0000-0003-0878-3831","position":3,"is_corresponding":false},{"id":1164612,"name":"Rita B. Aksenfeld","orcid":null,"position":4,"is_corresponding":false},{"id":841015,"name":"Elizabeth H. Jensen","orcid":null,"position":5,"is_corresponding":false},{"id":1164613,"name":"Yelena Koldobskaya","orcid":null,"position":6,"is_corresponding":false},{"id":1115249,"name":"Andrew Schacht","orcid":"0000-0002-7998-393X","position":7,"is_corresponding":false},{"id":1164116,"name":"Terry D. Kim","orcid":"0000-0001-7259-5486","position":8,"is_corresponding":false},{"id":356526,"name":"Priya Choudhry","orcid":"0000-0002-4438-1576","position":9,"is_corresponding":false},{"id":469736,"name":"Brett Lomenick","orcid":"0000-0002-5023-9998","position":10,"is_corresponding":false},{"id":344107,"name":"Spiros D. Garbis","orcid":"0000-0002-1050-0805","position":11,"is_corresponding":false},{"id":289199,"name":"Annie Moradian","orcid":"0000-0002-0407-2031","position":12,"is_corresponding":false},{"id":363255,"name":"Linda C. Hsieh‐Wilson","orcid":"0000-0001-5661-1714","position":13,"is_corresponding":false},{"id":567641,"name":"Matthew E. Griffin","orcid":"0000-0001-9549-4418","position":0,"is_corresponding":true}],"reference_count":135,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:18:47.408273Z","pmid":"37398272","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}