Fig. 1: Comprehensive workflow of mouse N-glycoproteomics study, including sample preparation, data analysis, neurodegeneration glycoproteomics and N-glycoproteome website. | Nature Communications

Fig. 1: Comprehensive workflow of mouse N-glycoproteomics study, including sample preparation, data analysis, neurodegeneration glycoproteomics and N-glycoproteome website.

From: Ultradeep N-glycoproteome atlas of mouse reveals spatiotemporal signatures of brain aging and neurodegenerative diseases

Fig. 1

Sample preparation: Five kinds of mouse tissues (brain, lung, kidney, liver, and heart) were studied. Three enzyme combinations (Trypsin, Trypsin coupled with Lys-C and Trypsin coupled with Glu-C) were applied for protein digestion. Two enrichment methods (ZIC-HILIC and Sepharose CL-4B) were utilized. A total of 154 raw over 936 h (39 days) were acquired with 6.8 million glyco-spectra (containing oxonium ions 204.0866). Diagrams of the mouse and tissues were created in BioRender. Kong, S. (2025) https://BioRender.com/k0n7j0g. Data Analysis: Four software (pGlyco3, StrucGP, MSFragger-Glyco, and Glyco-Decipher) were compared. Deep N-glycoproteomics analysis was conducted, showing the number of glycopeptides identified in different tissues. Micro-heterogeneity and tissue specificity was exhibited. Neurodegeneration Glycoproteomics: temporal and spatial brain glycoproteome analyses were performed, comparing control, Parkinson’s disease, and Alzheimer’s disease states at different ages (3 and 9 months). Multiple brain regions, including hippocampus (HPC), prefrontal cortex (PFC), substantia nigra (SN), and striatum (STR), were analyzed. Glycoproteome Website: The results were available on a dedicated N-glycoproteome website, featuring experimental N-glycoproteome data.

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