Epigenetic modifications of chromatin are essential in the regulation of many biological processes.The evolutionary conserved histone proteins that are intimately associated with DNA to form the chromatin are pivotal substrates herein. Until recently, research has been very targeted and mainly focused on the amino-terminal tail of these histones that protrude from the nucleosome and can become modified by many different posttranslational modifications (PTM). Here, we will apply the latest in bottom-up mass spectrometry data independent acquisition (DIA) strategies as a complementary approach to conventional data-directed acquisition (DDA) strategies to simultaneously map hundreds to thousands of PTM combinations in a quantitative manner and to generate a first bird’ eye view of the so-called “istone code”in differentiating human embryonic stem cells(hESC).

More specifically, UDMSE (Waters) and SWATH (ABSciex) acquisition strategies will be optimized for the task of coping with the combinatorial complexity of these modifications. This will encompass optimizing acquisition parameters, increasing identification efficiency and validating quantitative accuracy to finally map the most important histone epigenetic changes during the generation of primordial germ cells from hESC.