Plasmodium berghei strain NK65 is a rodent malaria parasite species widely used as a model of the human-infectious malaria parasite. Because a rodent malaria parasite model allows issues to be addressed which would not be possible with human-infectious species, e.g., mode of action and in vivo screening, a convenient method to analyze the malaria parasite proteome is required. The proteins of P. berghei separated using two-dimensional polyacrylamide gel electrophoresis were analyzed using matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight tandem mass spectrometry.