Here, we introduce protein-lipidation quantitation (PLQ)-the first method for quantitative analysis of both a substrate and a product of protein lipidation in a biologically relevant context. Such analysis is required to study roles of protein lipidation in cellular regulation. In PLQ, the substrate is fused with a fluorescent protein to facilitate quantitative detection of both the nonlipidated substrate and the lipidated product. When expressed in cells with endogenous lipidation activity, the substrate is intracellularly lipidated. Following cell lysis and sampling crude cell lysate for analysis, the substrate and the product are separated by surfactant-mediated capillary electrophoresis (CE) and quantitated by integrating fluorescence intensity over respective CE peaks. In this work, we prove PLQ in principle and demonstrate its robustness to changes in structures of the substrate and lipid donor. Finally, PLQ analysis confirms a hypothesized link between a mutation in p53 and cellular prenylation activity.