Relative quantification of acetylated histone peptides in HAP1 cells after treatment with MS-275

In a previous exploratory mass spectrometry experiment, we unravelled multiple histone and non-histone deacetylation targets of class I HDACs following acetyl-enrichment. Here, using targeted mass spectrometry without prior acetyl-enrichment, we validated selected histone targets in HAP1 cells treated for various time points with the HDAC1, HDAC2 and HDAC3 specific inhibitor MS-275. We confirmed significantly increased signals upon MS-275 treatment for 20 out of 21 selected acetylated peptides of histones H2A.V, H2B type 1-K/1-F, H3.3 and H4. The abundance of most of the selected acetylated peptides was increased already upon 6 hours of MS-275 treatment, and further increased after 24 hours. In summary, this validation experiment demonstrates the reliability of previous targeted approach and gives an additional insight in the the dynamics of acetylation increases following catalytic inactivation of HDAC1, HDAC2 and HDAC3.