Drosophila eyes have been an essential biological system for elucidating sensory signaling principles. The organization of the Drosophila compound eye, which brings about an optical phenomenon called Deep-Pseudo-Pupil (DPP), has been extensively studied in cutting-edge genetic and developmental studies. The detailed photochemical cycle of bistable photopigments has been studied in Drosophila using a genetic approach combined with electrophysiological in vivo screening protocols, which search for changes in the Prolonged-Depolarizing-Afterpotential (PDA) and Early-Receptor-Potential (ERP) phenomena. Genetic screening has contributed to the discovery of novel proteins necessary for many physiological processes. Notable examples are the inactivation-no-afterpotential D scaffold-protein and the light-activated channel transient receptor potential (TRP) and its homologue (TRPL), the founding members of the widely-spread and extensive TRP channel superfamily. Reversible light-dependent translocation of TRPL was discovered in the Drosophila eye using the DPP and immunocytochemistry, while light-dependent phosphorylation of phototransduction proteins were studied using mass spectroscopy and phosphor-specific antibodies. The genetic approach has also revealed the phosphoinositide-cycle, which drives the activation of light-activated channels. Lipidomics has thus became a key technique for understanding the functional consequences of defective proteins involved in the phosphoinositide-cycle. This collection will describe major techniques for investigating the localization and function of Drosophila retinal signaling-proteins, including important advice on the inherent difficulties hidden in these preparations. This collection should be also beneficial to scientists outside this field of research as these techniques can be adapted to other biological preparations.