A Waters Acquity H-class UPLC coupled with a Thermo TSQ Quantum Access triple quadrupole mass spectrometer was used to quantify the acetylated lysines on H3 and H4 peptides. The UPLC and MS/MS settings, solvent gradient, and detailed mass transitions were reported in our previously published work [40 (link),52 (link),53 (link)] and Table 1. Retention time and specific mass transitions were both used to identify individual acetylated and/or propionylated peptides. The areas under individual resolved peaks were integrated using Xcalibur software (version 2.1, Thermo). Relative quantitative analysis was used to determine the amount of acetylation on individual lysines [52 (link),53 (link)], and the time course kinetics of Piccolo NuA4-mediated acetylation for individual lysines can be plotted. We also noted that the ionization efficiency of H4 tail peptide (K5-R17) is about 10-fold less than that of H3 K9-R17 peptide. Thus, the samples of low concentration titrations (< 3 µM) have to be concentrated for the detection of histone acetylation.