Mass spectrometry based proteomics has revolutionized many aspects of modern biological research. One key area where mass spectrometry continues to significantly contribute is in the analysis of histone post-translational modification (PTM) patterns. Dynamic histone PTMs are known to be intricately associated with gene regulation (both activating and silencing), and also with epigenetic processes, therefore, accurate qualitative and quantitative mapping of modification sites on these proteins is of immense value. Mass spectrometry has been utilized to confirm, discover, quantify and determine the simultaneous combination of histone PTMs from many organisms. Here the recent mass spectrometry based studies of histone variants and the characterization of their modifications is reviewed.