This chapter presents methods for capillary electrophoresis (CE) fingerprinting of proteins in a cell extract and in single cells. A custom-made CE instrument with laser-induced fluorescence (LIF) detection, used for the analyses, is described. Detailed procedures are given for: (1) on column labeling of proteins with a fluorogenic reagent, 5-furoyl quinoline-3- carboxaldehyde, (2) CE separation of labeled proteins, (3) preparation of a protein extract from cultured cells, and (4) manipulations associated with analyses of proteins in single cells. More than 20 relevant publications are cited in this chapter to assist the reader with adopting the presented methods.
