Hydrophilic magnetic covalent organic frameworks for highly integrated pre-enrichment and analysis of colorectal cancer differential glycoproteomics

Finding glycoproteins related to both biomarkers and therapeutic targets is essential prerequisite. Unfortunately, the glycoproteins are hard to directly detect by mass spectrometry due to their low abundance and abundant of interferents. Herein, we report a systematic integration of enrichment and comparative analysis strategy using the hydrophilic magnetic covalent organic frameworks (COFs) as the platform to fish the glycopeptides from normal and colorectal cancer (CRC) cell lysates by bottom-up methods. The layer of COF was controlled growth on the surface of Fe3O4 nanoparticles and the hydrophilicity increased with L-cysteine (L-Cys) was modified. The Fe3O4@PVP/[email protected] nanoparticles have exhibited the excellent selectivity (IgG/BSA, 1:2000) and high sensitivity (0.1 fmol) for glycopeptide enrichment. A total of 214 glycopeptides and 597 glycosites belonged to 289 glycoproteins were enriched in FHC cell lysate by magnetic COFs. And 711 glycopeptides, 824 glycosites belonged to 440 N-glycoproteins were enriched in HT-29 cell lysate. Furthermore, the differential glycoproteins were comparatively analyzed through gene ontology for verifying biomarkers (LGALS3BP, PDIA3, etc.), therapeutic targets (TM9SF3, etc.), CRC pathological process, and differential glycoprotein’s function. This strategy bridges the enrichment technology and clinical requirements, has great potential for helping illuminate the mapping of CRC differential glycoproteomics.