Discovery of molecular targets for development of new insecticides and drugs is critical for successful control of a variety of insect pests and infectious diseases. The extensive databases for genome sequences of insect, microorganisms and viruses provide valuable information for identification of new targets.  Here, we report a discovery platform that utilizes bioinformatics, genomics and proteomics for high-throughput gene and protein target identification. The platform facilitates screening of customized cDNA libraries and the construction of protein expression panels. The customized gene libraries allow for gene-based selection of cell-surface proteins whose critical cellular functions are prioritized by their potential as insecticide targets. The protein expression panels contain individual transgenic insect cell lines formatted in multi-well plates, which are suitable for high-throughput screening of multiple insecticide targets. The advantage of the discovery platform is that it brings together genome- and proteome-based target identification and target-directed screening for validating the action of new compounds in cell-based assays.