Top-down Sequencing of Intact Proteoforms using the timsOmni mass spectrometer: Accurate Determination of Co-occurring Histone Modifications

Deep characterization of intact proteoforms remains an analytical challenge in functional proteomics, particularly for heterogenous multi-site post-translational modifications at distinct amino acid residues. Histones are among the most dynamically and diversely post-translationally modified proteins in eukaryote cells, carrying multiple, co-occurring and reversible modifications that can give rise to isomeric proteoform species. Tandem mass spectrometry with multimodal fragmentation capabilities is a promising approach for deep characterization of intact proteoforms, such as modified histones. We applied the novel timsOmni mass spectrometer, which incorporates the Omnitrap platform enabling multimodal MSⁿ workflows, for residue-level mapping of histone modifications, including acetylation and methylation. Recombinant histones H3.1 and H4 were in vitro acetylated by enzymes GCN5, PCAF and p300 to generate mono- and multi-acetylated proteoforms. Complementary MS ² electron- and collision-based dissociation (ECD, EID, _R CID and ECciD), together with MS ³ strategies, produced complete or near-complete backbone fragmentation of intact protein ions (>92% amino acid sequence coverage). For monoacetylated species generated by the more site-selective lysine acetyltransferases, the dominant proteoform matched the known catalytic preferences of the enzymes (H3.1K14ac for GCN5 and PCAF, and H4K8ac for PCAF), while minor positional isomers were also identified and their relative abundance estimated. In contrast, the broader substrate specificity of p300 produced a wide distribution of H4 proteoforms bearing up to seven acetylated lysine residues. Species carrying six and seven acetylations were characterized by multimodal MS ² /MS ³ experiments, enabling localization of individual acetylation sites and discrimination of positional isomers. Finally, endogenous histone proteoforms from liver extracts were analyzed, yielding sequence coverages of 92–93% for the most abundant species and enabling confident localization of multiple PTMs (acetylation and methylation). These results illustrate that multimodal MS ⁿ fragmentation of intact proteins supports residue-level assignment of combinatorial histone marks and coexisting positional isomers.