Workflow for proteomic analysis of purified lysosomes with or without damage v2

Lysosomes are a major degradative organelle within eukaryotic cells. Previous work has developed a method wherein the TMEM192 protein is tagged on its C-terminus with an epitope tag in order to immunopurify (IP) lysosomes from cell extracts.1 This process is referred to as Lyso-IP. Such lysosomes can be used for proteomic analysis or for metabolomic analysis. The Lyso-IP is adapted from a previous reported method (Wyant et al., 2018). Here we also describe processing steps using proteomics after lysosome purification in the context of lysosomal damaging agents. Agents such as L-Leucyl-L-Leucine methyl ester (hydrochloride) (LLoMe) and Gly-Phe-β-naphthylamide (GPN) induce lysosomal damage, leading to the degradation of damaged lysosomes by lysophagy. This adaptation of Lyso-IP provides a route to identify proteins that are recruited to damaged lysosomes using quantitative proteomics.