The proteomes of three heads of individual Drosophila melanogaster organisms have been analyzed and compared by a combination of liquid chromatography, ion mobility spectrometry, and mass spectrometry approaches. In total, 197 proteins are identified among all three individuals (an average of 120 +/- 20 proteins per individual), of which at least 101 proteins are present in all three individuals. Within all three datasets, more than 25 000 molecular ions (an average of 9000 +/- 2000 per individual) corresponding to protonated precursor ions of individual peptides have been observed. A comparison of peaks among the datasets reveals that peaks corresponding to protonated peptides that are found in all heads are more intense than those features that appear between pairs of or within only one of the individuals. Moreover, there is little variability in the relative intensities of the peaks common among all individuals. It appears that it is the lower abundance components of the proteome that play the most significant role in determining unique features of individuals.