Histone datasets for evaluation of histone extraction protocols

Extracting histones from cells is a routine operation for studies that aim to characterize histones and their post-translational modifications (hPTMs). However, label-free quantitative mass spectrometry (MS) approaches, both data-dependent (DDA) and data-independent (DIA), require streamlined protocols that are highly reproducible even at the peptide level, to enable simultaneous accurate quantification of dozens to hundreds of these hPTMs. We present a step-by-step comparison of different histone extraction protocols based on literature and evaluate their suitability for label-free MS purposes using a nanoESI label-free MS1 intensity-based DDA MS experiment. We evaluate the data both using a targeted and an untargeted (Progenesis QI) approach.