An Online Buffer Exchange Platform for Charge Detection Mass Spectrometry Analysis of AAVs and AAV-Antibody Complexes

Adeno-associated viruses (AAVs) are leading vectors in gene therapy that have demonstrated great potential in combating a wide range of human diseases. To enhance specificity and reduce dosing requirements, antibody-retargeted AAVs have emerged as a promising strategy to redirect vectors to novel receptors, thereby achieving improved efficacy and safety. However, effective characterization of AAVs and AAV-antibody complexes is complicated by heterogeneities that arise from variations in capsid protein assembly, genome integrity, and antibody decorations, demanding high-resolution techniques beyond traditional methods. Charge detection mass spectrometry (CDMS) is an emerging technique that effectively characterizes complex AAV samples by directly measuring ion charge. This technique is typically performed using static infusion-based nanoelectrospray ionization with long acquisition times, which is highly manual and subject to unstable spray and sample instability. To address limitations of static infusion in CDMS, we have developed a novel automated platform: size-exclusion chromatography-based flow injection coupled with CDMS (SEC-FI-CDMS). This platform streamlines and automates sample introduction with a dual-flow setup, enabling fast online desalting in high-flow mode and stable, prolonged infusion in low-flow mode for Orbitrap-based CDMS analysis. It accurately determines AAV genome packaging ratios and masses, differentiates capsid assembly and payload variations, and resolves antibody decoration on AAV-antibody complexes. This comprehensive characterization supports AAV manufacturing and development, paving the way for more effective next generation gene therapies.