Apoptosis and autophagic cell death are the two most prominent forms of programmed cell death that occur during animal development. While much is known about the regulation of apoptosis, relatively little is known about the mechanisms underlying autophagic cell death, and what mechanism and biochemical changes distinguish these most prominent forms of physiological cell killing. Drosophila embryos and salivary glands are an ideal system to study apoptosis and autophagic programmed cell death. The mass of embryos and salivary gland cells enable rapid purification and separation from other tissues, providing one of the few higher animal genetic systems where molecular and biochemical approaches can be used to study a purified population of dying cells in the context of a developing organism. These attributes argue that studies of Drosophila apoptosis and autophagic cell death will lead to the identification of new cell death proteins, and provide an excellent system to study their function. The programmed cell death genetic pathway is extremely conserved between fruit flies and humans, indicating that studies of cell death in Drosophila will be directly relevant to higher organisms. Our research goal is to develop, optimize, and apply innovative proteome technology for the comprehensive analysis of protein profiles during programmed cell death. By using the fruit fly Drosophila melanogaster as a model system, these proteome studies will explore pathways and identify biomarkers associated with Caspase activation during cell death in developing animals. This challenge will be addressed through the development and application of a capillary-based and integrated top-down/bottom-up multidimensional separation platform capable of ultrahigh resolution of intact proteins, followed by in situ proteolytic digestion of size-resolved proteins, high throughput peptide separation, and ultrasensitive peptide/protein identification. The combined strength of Drosophila genetics and the proposed innovative bioanalytical technologies enables investigation into the regulation of programmed cell death at the genome-wide level including the expression of proteins on a global scale.