{"doi":"10.1016/j.jprot.2023.104896","title":"Proteomic and N-glycoproteomic analyses of total subchondral bone protein in patients with primary knee osteoarthritis","abstract":null,"journal":"Journal of Proteomics","year":2023,"id":601023,"datarank":0.29188652235829704,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.0,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":579269,"name":"Yong Zhou","orcid":"0000-0001-9751-3141","position":1,"is_corresponding":false},{"id":1540946,"name":"Jiangbo Yan","orcid":"0000-0001-5019-346X","position":2,"is_corresponding":false},{"id":245122,"name":"Zheng Wang","orcid":"0000-0003-4471-5983","position":3,"is_corresponding":false},{"id":533515,"name":"Yong Yang","orcid":"0000-0002-9928-7165","position":4,"is_corresponding":false},{"id":1540947,"name":"Weidong Zhao","orcid":null,"position":5,"is_corresponding":false},{"id":954104,"name":"Na Wang","orcid":"0009-0006-9921-6478","position":6,"is_corresponding":false},{"id":1540949,"name":"Zhidong Lu","orcid":null,"position":7,"is_corresponding":false},{"id":1540951,"name":"Yaogeng Chen","orcid":null,"position":8,"is_corresponding":false},{"id":1540952,"name":"Qunhua Jin","orcid":"0000-0001-7616-3357","position":9,"is_corresponding":false},{"id":1540945,"name":"Gangning Feng","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Proteomic and N-glycoproteomic analyses of total subchondral bone protein in patients with primary knee osteoarthritis","abstract":"N-glycosylation is an important post-translational modification necessary to maintain the structural and functional properties of proteins. Impaired N-glycosylation has been observed in several diseases. It is significantly modified by the state of cells and is used as a diagnostic or prognostic indicator for multiple human diseases, including cancer and osteoarthritis (OA). Aim of the study was to explore the N-glycosylation levels of subchondral bone proteins in patients with primary knee OA (KOA) and screen for potential biological markers for the diagnosis and treatment of primary KOA. A comparative analysis of total protein N-glycosylation under the cartilage was performed in medial subchondral bone (MSB, N = 5) and lateral subchondral bone (LSB, N = 5) specimens from female patients with primary KOA. To analyse the N-glycosylation sites of the proteins, non-labelled quantitative proteomic and N-glycoproteomic analyses were performed based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) data. Parallel reaction monitoring (PRM) validation experiments were carried out on differential N-glycosylation sites of proteins in selected specimens, including MSB (N = 5) and LSB (N = 5), from patients with primary KOA. In total, 1149 proteins with 1369 unique N-chain glycopeptides were detected, and 1215 N-glycosylation sites were found, in which ptmRS scores for 1163 N-glycosylation sites were ≥ 0.9. In addition, N-glycosylation of the total protein in MSB compared to that in LSB was identified, in which 295 N-glycosylation sites were significantly different, including 75 upregulated and 220 downregulated N-glycosylation sites in MSB samples. Importantly, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses of proteins with differential N-glycosylation sites showed that they were primarily associated with metabolic pathways including ECM-receptor interactions, focal adhesion, protein digestion and absorption, amoebiasis, and complement and coagulation cascades. Finally, PRM experiments confirmed the N-glycosylation sites of collagen type VI, alpha 3 (COL6A3, VAVVQHAPSESVDN[+3]ASMPPVK), aggrecan core protein (ACAN, FTFQEAAN[+3]EC[+57]R, TVYVHAN[+3]QTGYPDPSSR), laminin subunit gamma-1 (LAMC1, IPAIN[+3]QTITEANEK), matrix-remodelling-associated protein 5 (MXRA5, ITLHEN[+3]R), cDNA, FLJ92775, highly similar to Homo sapiens melanoma cell adhesion molecule (MCAM), mRNA(B2R642, C[+57]VASVPSIPGLN[+3]R), and aminopeptidase fragment (Q59E93, AEFN[+3]ITLIHPK) in the array data of the top 20 N-glycosylation sites. These abnormal N-glycosylation patterns provide reliable insights for the development of diagnostic and therapeutic methods for primary KOA.","is_dataset_classified":null,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"37024074","pmcid":null,"openalex_id":"https://openalex.org/W4362636723","authors":[],"funders":[{"funder_name":"National Natural Science Foundation of China","grant_id":"U22A20285","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"82060331","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"N0.U22A20285","title":null},{"funder_name":"Ningxia Hui Autonomous Region Natural Science Foundation","grant_id":"2020AAC03123","title":null},{"funder_name":"Ningxia Hui Autonomous Region Natural Science Foundation","grant_id":"2021A0478","title":null},{"funder_name":"Ningxia Medical University","grant_id":"","title":null}],"total_grants":6,"fwci":0.5594,"citation_percentile":0.60617878,"influential_citations":0,"citation_trend":[{"year":2024,"count":2},{"year":2025,"count":4}],"oa_status":"hybrid","license":"cc-by-nc-nd","oa_locations":[{"url":"https://doi.org/10.1016/j.jprot.2023.104896","host_type":"journal"},{"url":"https://doi.org/10.1016/j.jprot.2023.104896","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S1874391923000854?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S1874391923000854?httpAccept=text/plain","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/37024074","host_type":"repository"}],"fields_of_study":["Glycosylation and Glycoproteins Research","Peptidase Inhibition and Analysis","Protease and Inhibitor Mechanisms"],"mesh_terms":["Chromatography, Liquid","Female","Humans","Knee Joint","Osteoarthritis, Knee","Proteomics","Tandem Mass Spectrometry"],"keywords":["Glycosylation","Osteoarthritis","N-linked glycosylation","Chemistry","Tandem mass spectrometry","Glycoprotein","Molecular biology","Biochemistry","Medicine","Biology","Pathology","Mass spectrometry","Chromatography","Glycan","Proteomics","Subchondral Bone","N-glycoproteomics","Primary Knee Osteoarthritis"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"uniprot"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-29T14:53:20.137298Z","pmid":null,"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":[]}