The histidine-rich protein II (HRP II) from Plasmodium falciparum is an unusual protein composed of 40% alanine, 36% histidine, and 11% aspartate residues. Expression of HRP II in Escherichia coli results in the isolation of a heterogeneous protein. Mass spectrometry reveals a reduction in mass by multiples of 9 Da from the expected molecular mass that can be attributed to the substitution of glutamine for some histidine residues in the sequence. The extent of the glutamine for histidine substitution can be reduced by slowing the expression rate. Mass spectral analysis of HRP II also revealed alpha-amino methylation of the N-terminal alanine residue of HRP II.