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With promising advances in structural and site\u2010specific glycoproteomics, how to thoroughly extract important information from these multi\u2010dimensional data has become another unresolved issue. The present study reports a comprehensive data mining strategy to systematically extract overall and altered glycan features from quantitative glycoproteome data. By applying the strategy to investigation\u00a0of thymic involution, the study not only presents a high\u2010resolution glycoproteome map of the mouse thymus, displaying distinct glycan structure patterns among immune\u2010relevant cellular components, but also uncovers four major altered glycan features associated with thymic involution, including elevated LacdiNAc mainly on the MHC class I complex, increased sialoglycans that perform multiple immune functions, down\u2010regulated bisecting glycans mostly linked to a sole GlcNAc branch, as well as possible shifts of glycan structures at the same glycosites. Regulatory network analyses further reveal the coordinated interactions of altered glycans with upstream regulators, including glycosyltransferases, glycosidases, and glycan\u2010binding proteins, as well as downstream signaling pathways. These data offer valuable resources for future functional studies on glycosylation and the mechanistic investigation of thymic involution, supporting the strategy as a powerful tool for in\u2010depth mining of structural and site\u2010specific glycoproteome data from various biomedical samples.<\/jats:p>","DOI":"10.1002\/advs.202502013","type":"journal-article","created":{"date-parts":[[2025,7,24]],"date-time":"2025-07-24T11:30:09Z","timestamp":1753356609000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["A Glycoproteome Data Mining Strategy for Characterizing Structural Features of Altered Glycans with Thymic Involution"],"prefix":"10.1002","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2747-9480","authenticated-orcid":false,"given":"Zhida","family":"Zhang","sequence":"first","affiliation":[{"name":"Laboratory for Disease Glycoproteomics College of Life Sciences Northwest University  Xi'an 710069 P. 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