biostudies-literatureDu CNational Institutes of HealthNational Institute of General Medical SciencesNIGMS NIH HHS13889-13896https://www.ebi.ac.uk/biostudies/studies/S-EPMC10874503biostudies-literatureUnknown95(37)Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (<i>m</i>/<i>z</i>). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fraAnalytical chemistryCombining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes.PMC10874503P41GM128577P41 GM128577P41GM108569P41 GM108569RM1 GM149374Cleary SPJones BJWysocki VHDu CKafader JOKostelic MMfalseCombining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes.Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (<i>m</i>/<i>z</i>). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fra2023-01-01T00:00:00Z2023 Sep2026-07-15T05:19:48.853Z2025-04-04T01:38:18.44ZS-EPMC108745033767263210.1021/acs.analchem.3c02185