A mass spectrometry-based workflow to analyze histone post-translational modifications and the associated acid extractome

Worldwide, there is an increasing interest in epigenetics because of its involvement in several diseases. An important epigenetic mechanism is the histone post-translational modifications and the histone code they generate. Mass spectrometry (MS) offers the opportunity to comprehensively characterize the histone code in one single experiment. We developed a workflow that allows starting from a cell pellet to: 1) extract the histones, 2) analyze them via bottom-up proteomics using data-dependent acquisition (DDA) mass spectrometry, and 3) identify and quantify them via our data analysis pipeline. The time required to complete the entire workflow is highly dependent on the number of samples to be analyzed and should be considered as at least 1 week of sample preparation prior to the acquisition, approximately 90 minutes of acquisition time per sample and thereafter one to several weeks of data analysis depending on the complexity of the data.