The dinuclear copper complex (alpha-cyano-4-hydroxycinnamic acid (CHCA) copper salt (CHCA)(4)Cu(2)), synthesized by reacting CHCA with copper oxide (CuO), yields increased abundances of [M + xCu - (x-1)H](+) (x = 1-6) ions when used as a matrix for matrix-assisted laser desorption ionization (355 nm Nd:YAG laser). The yield of [M + xCu - (x-1)H](+) (x = 1 to approximately 6) ion is much greater than that obtained by mixing peptides with copper salts or directly depositing peptides onto oxidized copper surfaces. The increased ion yields for [M + xCu - (x-1)H](+) facilitate studies of biologically important copper binding peptides. For example, using this matrix we have investigated site-specific copper binding of several peptides using fragmentation chemistry of [M + Cu](+) and [M + 2Cu - H](+) ions. The fragmentation studies reveal interesting insight on Cu binding preferences for basic amino acids. Most notable is the fact that the binding of a single Cu(+) ion and two Cu(+) ions are quite different, and these differences are explained in terms of intramolecular interactions of the peptide-Cu ionic complex.