Automated Sample Preparation for the Multiplexed Analysis of Single-Cell Histone Post-Translational Modifications (sc-hPTM2)

Histone post-translational modifications (hPTMs) are central regulators of chromatin organization and gene expression. Their dysregulation is implicated in development, cancer, and aging. While mass spectrometry is the method of choice to study hPTMs, most protocols are designed for bulk samples and cannot resolve cell-to-cell variability. Extending histone PTM analysis to the single-cell level is therefore essential but technically challenging, as histones are low in abundance, lysine-rich, and heavily modified. Here, we describe an automated single-cell proteomics workflow for histone PTM analysis using nano liquid handling. The system enables nanoliter-scale processing of individual cells with minimal handling and high reproducibility. The workflow includes digestion with ArgC Ultra protease, which cleaves at arginine residues and avoids the need for lysine-blocking derivatization steps typically required in histone proteomics. To enable quantitative comparison between conditions, we apply a two-plex labeling strategy with propionic anhydride and its deuterated analogue, propionic anhydride-d10. This combination of automated sample preparation, isotopic multiplexing, and ArgC Ultra digestion results in a streamlined and sensitive protocol for single-cell histone PTM analysis. The method allows for the investigation of chromatin heterogeneity and the effects of epigenetic perturbations at single-cell resolution. To demonstrate the workflow, we generated spheroids from HepG2/C3A hepatocellular carcinoma cells and treated them with sodium butyrate, a histone deacetylase inhibitor that induces hyperacetylation.