Peptide Mapping Of Adeno Associated Virus Capsid Proteins

By Lorne Nelson, Mastooreh Chamanian, PhD, Roxana Eggleston-Rangel, and Bryan Tackett, PhD

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AAV-based gene therapies depend on capsid proteins that are both structurally complex and vulnerable to post-translational modifications that may influence stability, assembly, and therapeutic performance. Peptide mapping offers a practical way to characterize these viral proteins, even with the added challenge of homologous VP1, VP2, and VP3 sequences within the 60-protein capsid. Using tryptic digestion and reversed-phase LC-MS, AAV5 and AAV9 capsid peptides can be profiled with strong sequence coverage—93.6% for AAV5 and 92.7% for AAV9—supporting deeper evaluation of capsid identity and modification patterns.

Access the full application note to review the sample preparation workflow, LC-MS conditions, and peptide mapping results for both serotypes.