N-terminal acetylation is one of the most common protein modifications in eukaryotes. The NatA complex is the dominant regulator of the N-acetylome in all eukaryotes. The Huntingtin yeast partner K (HYPK) physically interacts with the NatA/NAA50 comples in metazoan and we describe HYPK as a critical regulator of NatA acivity. This proteome dataset compares the HYPK mutation Arabidopsis lines hypk-1 and hypk-3 to wild type Arabidopsis.