Abstract
LIR motif-containing proteins (LIRCPs) bind to LDS (LIR motif docking site) of Atg8-family proteins. In this protocol, we describe steps to identify Drosophila LIRCPs, in Atg8a LDS mutants we have created, via label-free quantitative proteomic analysis. We detail steps for extraction of proteins from adult Drosophila heads, followed by liquid chromatography-mass spectrometry (LC-MS/MS) analysis. We also describe screening steps of upregulated proteins in Atg8a LDS mutants, leading to identification of novel LIRCPs in Drosophila. For complete details on the use and execution of this protocol, please refer to Rahman et al. (2022).