Protein-based radicals generated in the reaction of ferricytochrome c (cyt c) with H 2 O 2 were investigated by electrospray mass spectrometry (ESI-MS) using 3,5-dibromo-4-nitrosobenzenesulfonate (DBNBS). Up to four DBNBS-cyt c adducts were observed in the mass spectra. However, by varying the reaction conditions (0 -5 molar equivalents of H 2 O 2 and substituting cyt c with its cyanide adduct which is resistant to peroxidation), noncovalent DBNBS adduct formation was inferred. Nonetheless, optical difference spectra revealed the presence of a small fraction of covalently trapped DBNBS. To probe the nature of the noncovalent DBNBS adducts, the less basic proteins, metmyoglobin (Mb) and ␣-lactalbumin, were substituted for cyt c in the cyt c/H 2 O 2 /DBNBS reaction. A maximum of two DBNBS adducts were observed in the mass spectra of the products of the Mb/ H 2 O 2 /DBNBS reactions, whereas no adducts were detected following ␣-lactalbumin/H 2 O 2 /DBNBS incubation, which is consistent with adduct formation via spin trapping only. Titration with DBNBS at pH 2.0 yielded noncovalent DBNBS-cyt c adducts and induced folding of acid-denatured cyt c, as monitored by ESI-MS and optical spectroscopy, respectively. Thus, the noncovalent DBNBS-cyt c mass adducts observed are assigned to ion pair formation occurring between the negatively charged sulfonate group on DBNBS and positively charged surface residues on cyt c. The results reveal the pitfalls inherent in using mass spectral data with negatively charged spin traps such as DBNBS to identify sites of radical formation on basic proteins such as cyt c.Reactive oxygen species, such as H 2 O 2 and superoxide, are generated by all aerobic cells as by-products of a number of metabolic reactions and in response to various stimuli. Oxidative damage can occur when H 2 O 2 reacts with heme proteins, such as ferricytochrome c (cyt c), 1 to form highly reactive oxyferryl-heme and transient protein-based radical species (X ⅐ ) that are linked to the initiation of lipid peroxidation (1, 2). Detection of X ⅐ in biological systems is often difficult because they are short-lived and highly reactive. Spin traps, which are diamagnetic compounds containing a functional group that reacts with X ⅐ to form a more stable paramagnetic adduct (XST ⅐ ), are frequently used in electron paramagnetic resonance (EPR) investigations (3). Although EPR signals can provide information about a radical center and its environment, the specific sites of radical formation in biomolecules are not identified. Coupling of high performance liquid chromatography (HPLC) and mass spectrometry (MS) has been used to identify spin adducts of various small molecules (4 -6). Our research group has extended the use of LC/MS of spin adducts to proteins to overcome the inherent limitations of EPR. We have found that conversion of the spin adduct XST ⅐ to a stable diamagnetic mass adduct (XMA) via ascorbate reduction permits the assignment of XMA to a specific amino acid residue when spin trapping and peptide mass mapping by ...