Here we discuss proteomic analyses of whole cell preparations of the mosquito stages of malaria parasite development (i.e.
gametocytes, microgamete, ookinete, oocyst and sporozoite) of Plasmodium berghei. We also include critiques of the
proteomes of two cell fractions from the purified ookinete, namely the micronemes and cell surface. Whereas we summarise
key biological interpretations of the data, we also try to identify key methodological constraints we have met, only some of
which we were able to resolve. Recognising the need to translate the potential of current genome sequencing into functional
understanding, we report our efforts to develop more powerful combinations of methods for the in silico prediction of
protein function and location. We have applied this analysis to the proteome of the male gamete, a cell whose very simple
structural organisation facilitated interpretation of data. Some of the in silico predictions made have now been supported by
ongoing protein tagging and genetic knockout studies. We hope this discussion may assist future studies.