Histone proteins are the structural components of nucleosomes, which form chromatin. Histone proteins are typically modified with many posttranslational modifications (PTMs), which affect chromatin accessibility, and by extension, modulate gene transcription, and other DNA-related processes. Mass spectrometry has become the reference technology to quantify global levels of hundreds of histone PTMs in single experiments. The advancement of high throughput has paved the way to new possibilities, including experimental design that include large cohort of samples. In this chapter, we describe a protocol for the unbiased analysis of histone PTMs assisted by a robotic liquid handler. The implementation of a simple-to-use script for automated histone derivatization and digestion reduces the number of manual steps needed to prepare histone peptides for mass spectrometry analysis and improves consistency of resulting data.