The metalloproteome is defined as the set of proteins that have metal-binding capacity by being metalloproteins or having metal-binding sites. A different metalloproteome may exist for each metal. Mass spectrometric characterization of metalloproteomes provides valuable information relating to cellular disposition of metals physiologically and in metal-associated diseases. We examined the Cu and Zn metalloproteomes in three human hepatoma lines: Hep G2 and Mz-Hep-1, which retain many functional characteristics of normal human hepatocytes, and SKHep-1, which is poorly differentiated. Additionally we studied a single specimen of normal human liver and Hep Metals play a pivotal role in cellular metabolism. They function as the catalytic centers in many biochemical reactions and serve as structural elements for a large number of regulatory proteins (1, 2). Characterization of metal-binding proteins is important for understanding the structure and biological functions of such proteins in metal-associated diseases. In the past few years, a variety of mass spectrometric techniques has been used to probe the metal-protein interactions in metal-containing proteins. These studies have been successfully applied to determining metal binding stoichiometry (3-9), metal-binding sites (10, 11), and metal-dependent structure/conformation changes (12,13). A number of metalbinding proteins, such as cytochrome c oxidase (14), albumin (3, 7), metallothionein (12,15,16), prion protein (PrP) (8,9,11,13,17), matrilysin (4, 5), and non-heme iron-containing metalloproteins (6), have been individually well characterized by either overall mass measurements on the intact metal-protein complexes or peptide sequencing on the protein digest with tandem mass spectrometry.Rapid developments in proteomic technology and bioinformatics have permitted identification of proteomes of cell lines and tissue by using mass spectrometry instrumentation (for review, see . The specific advances include the use of two-dimensional gel electrophoresis (2DE),