The oxidation of the lipid components of LDL has been studied extensively, but much less is known about the oxidation of the apoprotein. The modification of the apoprotein is likely to be a major determinant of the effects of oxidation of LDL on its function and on the process of atherogenesis. In addition, the oxidation of LDL offers an excellent model for the study of mechanistic details of the oxidative modification of proteins in mixed-phase systems. We reacted native and Cu-oxidized LDL with 2,4-dinitropheynylhydrazine (DNPH), delipidated and trypsinized the protein and analyzed the products by reverse phase HPLC. At 220 nm both native and Cu-oxidized LDL showed similar complex patterns of protein fragmentation in their tryptic digests. However, at 365 nm, which is characteristic of DNPH-derived hydrazones, the chromatograms of oxidized LDL showed several discrete peaks, whereas native LDL showed none. Oxidations of different samples of LDL have shown qualitative similarities, with some quantitative differences. We have isolated and obtained initial structural characterizations of selected prominent peaks from the 365 nm detection of the oxidized LDL. One peptide, LEGTTR, located between amino acids 3354 and 3359, belongs to the LDL receptor binding domain, which contains a cluster of basic amino acids, such as would favor binding of a redox-active transition metal for catalysis and site direction of the oxidation. This modification of LEGTTR is one of two HPLC peaks observed after only 1 h exposure to Cu-catalyzed oxidation. Our studies suggest a surprisingly selective process of oxidation of the apoprotein and describe an approach that should be useful for the characterization of the oxidation of other proteins as well.