StrucGAP: a modular, streamlined and traceable data mining platform for structural and site-specific glycoproteomics

The rapidly developing search engines for glycopeptide identification and accumulated high-resolution glycoproteomic data underscore the need for robust downstream data mining platforms towards subsequently functional and mechanistic studies. Here, we introduce StrucGAP, a Structural Glycoproteomics Analysis Platform for scalable downstream data mining of site-specific N-glycoproteomics. It integrates modules for data quality control, overall glycan structural characterization, altered glycan feature extraction, functional annotation, as well as upstream regulation and downstream networks. Its visualization and insight-tracking functionalities distill interpretation across hundreds of outputs, uniquely enabling to generate chart-based analysis reports and extract key glycosylation insights—capabilities rarely found in existing omics tools. Applying StrucGAP to an uncharacterized aging mouse uterus dataset reveals bidirectional regulation of core-fucosylation, and progressive, coordinated enrichment of glycans featuring sialylation via Neu5Ac, Lewis epitopes, and hybrid glycans along glycosylation dynamics. These changes are functionally linked to adhesion and remodeling, demonstrating StrucGAP’s ability to distill critical glycosylation insights from multi-dimensional information of structural N-glycoproteome datasets. StrucGAP is a structural glycoproteomics analysis platform that distills multi-dimensional information of glycoproteome datasets into structural and functional insights towards mechanistic studies.