Inflammation, although a necessary response to infection, may contribute to the pathogenesis of diseases such as bronchopulmonary dysplasia and necrotizing enterocolitis, presumably in part through the action of MPO and HOCl on tissue biomolecules. In studies of oxidation of low density lipoproteins (LDL) as a model for oxidation of cellular lipids and proteins, we have observed a series of relatively specific sites of amino acid oxidation on apoB-100 of LDL by HOCl, including oxidation of seven different Cys residues on apoB-100 to intermediates that form derivatives with 2,4-dinitrophenylhydrazine (DNPH). In addition, evidence for HOCl-oxidized LDL in human atherosclerotic lesions has been reported from studies using a monoclonal antibody specific for HOCl-treated LDL. From LDL oxidized by HOCl or by MPO in vitro, we separated by HPLC tryptic peptides showing absorbance at 365 nm, which is characteristic of the dinitrophenyl moiety. Mass spectral analyses indicated oxidation to methionine sulfoxide (M=O) and formation of the cysteinyl azo derivative (RSN=NAr) of EEL(*C)T(M=O)FIR, which implicates the corresponding sulfenyl chlorides or sulfenic acids, with subsequent oxidation to the azo species, although the product also can be rationalized through dehydration of the hydrazide formed from the sulfinic acid. Oxidation of LDL with MPO, Cl-, and H2O2 in vitro differed considerably from oxidation with HOCl in that the oxidation by MPO was remarkably selective for formation of a single DNPH-reactive peptide, which we separated and identified by mass spectrometry and N-terminal sequence analysis as VELEVPQL(*C)SFILK. The peptide EELCTMFIR was synthesized and exposed to HOCl in vitro, treated with DNPH, product peptides separated by HPLC, and analyzed by mass spectrometry. The analyses indicated conversion of the cysteine to the corresponding DNPH-derived sulfonamide, RSO2NHNHAr, presumably through the sulfonyl chloride, RSO2C1. The intermediates indicated by the respective DNPH derivatives would not be expected to be chemically stable in free solution, and the observation of the respective DNPH derivatives suggests significant effects of the protein microenvironment in LDL, which would be necessary to stabilize the reactive intermediates implicated by the present studies. These results demonstrate that alterations other than the formation of aldehydes and ketones may be significant in what has to date been called “protein carbonyls,” and reinforce the role of cellular thiols in antioxidant defense functions.