Nuclei were isolated from leaves of transgenic plants expressing HA-tagged H3.1 (HTR5) or H3.3 (HTR13). MNase treated nuclear extracts were used for immunoprecipitation with HA agarose beads (Roche). Immunoprecipitated proteins were analysed by 4-20% SDS-PAGE, silver stained, and protein bands corresponding to transgenic copy of H3 and endogenous H3 were used for trypsin and LysC digestion followed by LC-MS/MS.