Quantitative proteomic analysis of histone modifications

Histone post-translational modification (PTM), or histone mark, in combination with DNA modifications, histone variants, and ATP-dependent protein complex formation, is used by cells to dynamically modulate chromatin structure and function. These histone PTMs are proposed to contribute a 'histone code' or 'histone language' that dictates the functions of the proteins in gene expression and chromatin dynamics. The histone code can facilitate the recruitment of diverse chromatin remodeling enzymes to regulate chromatin dynamics. Conversely, chromatin remodeling enzymes can also influence the histone PTMs. Mass spectrometry (MS) technology is nowadays able to detect those histone marks with stoichiometry of 0.01% or higher. The MS-based quantification technologies, using labeling or label-free approaches, enable quantifying dynamic changes of histone marks. Peptide-bond fragmentation in MS, in combination with a suitable quantification technique, enables quantifying dynamic changes of PTMs under diverse cellular environments.