Site-specific and Quantitative N-glycan Heterogeneity Analysis of the Charge Isomers of an Anti-VEGF Recombinant Fusion Protein by High-resolution 2-dimensional Gel Electrophoresis and Mass Spectrometry.

Glycan modification prompts important concerns about the quality control of biopharmaceutical production. Conbercept is a multi-glycosylated recombinant fusion protein drug approved for the treatment of age-related macular degeneration (AMD). With 14 N-glycosites in the molecule and 7 N-glycosites in the monomer, the charge isomer separation and characterization of conbercept pose great challenges due to its enormous heterogeneities. The batch-to-batch stability on the charge isomer distribution and the possible causation of the pattern necessitate the development of effective analytical approaches. Here, the immobilized pH gradient (IPG)-based two-dimensional gel electrophoresis (2-DE) approach was first optimized to achieve high-resolution, high-reproducible separation and preparation of charge isomers. Then, combined with the quantitative analysis strategy of site-specific N-glycan heterogeneity based on the diagnostic MS2 ion (peptides+GlcNAc, Y1 ions) of glycopeptides, an integrated approach for the quantitation of site-specific N-glycan heterogeneities among charge isomers was established. Finally, the quantitation of site-specific N-glycoforms in each of the 2-DE resolved spots were performed, and the results showed that the sialylaion tends to increase for gel spots located in the acidic regions. This study provides an effective approach to separate the charge isomers of the heavily glycosylated protein drugs, and to quantitatively explore the site-specific N-glycans dynamics along with the different charge isomers.