Functional understanding of the nuclear envelope requires the identification of its component proteins and their interactions. Trypanosomes cause human and livestock diseases worldwide but are so divergent from animals and fungi that in silico searches for homologs of proteins are frequently of low value. Here we describe a strategy for the straightforward identification of nuclear envelope proteins from trypanosomes that classifies proteins and their interaction networks in the nuclear pore complex. Milling frozen whole cells into a powder and rapid screening of buffer conditions for optimization of complex isolation is described. The method is inexpensive and potentially applicable to many organisms, providing fast access to functional information.