Chromatin constitutes a highly dynamic regulatory framework that integrates developmental and environmental cues to control genome activity and maintain cellular identity. Disruption of chromatin architecture is a hallmark of numerous pathologies--from cancer to neurodegenerative disorders--and is intimately linked to aging. However, decoding chromatin-centered pathways remains technically formidable due to the extraordinary complexity of the underlying components, including diverse regulatory factors and a vast array of covalent modifications on histones, RNA, and DNA.

Mass spectrometry (MS)-based methods have played a foundational role in chromatin research, enabling the discovery of numerous epigenetic modifications and pathways. Recent advances in MS instrumentation, sample preparation, and data analysis allow chromatin to be examined with remarkable depth, including at single-cell resolution. These innovations are transforming the ability to interrogate chromatin dynamics, providing insights into regulatory mechanisms underlying diverse biological processes and disease states.

Compared to commonly used next-generation sequencing (NGS) and antibody-based approaches, MS offers several key advantages. For example, it enables unbiased detection of both known and novel chromatin modifications, supports quantitative analysis of thousands of analytes, and provides a versatile platform for studying a broad range of biomolecules, including proteins, metabolites, and nucleotides. These features make MS a cornerstone of modern chromatin biology.

To empower scientists in this rapidly evolving field, this Methods Collection presents detailed protocols for profiling protein and nucleic acid modifications, chromatin-associated factors, and small molecules. It aims to make MS-based workflows more accessible and reproducible across laboratories.