A method is described for radioiodination to high specific activity of fixed and stained proteins within sodium dodecyl sulfate-polyacrylamide gels, without elution of the proteins from the gel. Following radioiodination, the proteins can be removed from the gel by trypsin treatment and the peptides analyzed. This procedure offers a means to structurally compare the proteins of multicomponent systems when purification of each component to homogeneity is unfeasible. Using this technique, we have compared the tryptic peptides of all the major protein components of Moloney and Rauscher leukemia viruses using only 50 to 100 microgram of total protein from each virus. Additionally, we have analyzed the membrane proteins of Dictyostelium discoideum at various stages in development. The validity of the technique and its value as a tool for comparative studies and identification of precursor-product relationships is discussed.