Protocol for Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS: Sample Preparation, Data Acquisition and Analysis

Abstract The disassembly and digestion of nucleosome particles in current proteomics approaches forfeits correlations among histones and blurs nucleosome-level information. We developed Nuc-MS which analyzes whole nucleosomes and displays their histone modifications and variants in a single mass spectrum. In this protocol, we provide step-by-step instructions for preparation of mononucleosomes for mass spectrometry (MS) analysis, and parameter sets for Nuc-MS data acquisition and data analysis.