This paper describes the development of analytical methodology for the separation of naphthalene-2,3-dicarboxaldehyde (NDA)-derivatized substance P (CBI-SP) and five lysine-containing metabolites by micellar electrokinetic chromatography (MEKC). The effect of surfactant composition and organic modifiers on the separation was investigated. The final separation buffer consisted of 80 mM sodium cholate in 50 mu N-tris (hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES), pH 7. All six lysine-containing peptides were separated under these conditions.