Accurate Measurement of Formaldehyde-Induced DNA-Protein Cross-Links by High-Resolution Orbitrap Mass Spectrometry

Genomic instability caused by DNA-protein cross-link (DPCs)-induced DNA damage is implicated in disease pathogenesis, aging, and cancer development. The covalent linkages between DNA and protein are induced by chemical reactions catalyzed by the endogenous metabolic intermediates and exogenous agents, such as aldehydes, chemotherapeutic agents, and ionizing radiation. Formaldehyde has been classified as a genotoxic carcinogen. In addition, endogenous formaldehyde-induced DPCs may increase the risks of bone marrow toxicity and leukemia. There is a need to develop an effective detection method for DPC analysis, including the structural differentiation of endogenous and exogenous formaldehyde-induced DPCs. To this end, our group previously reported a useful liquid chromatography-selected reaction monitoring (LC-SRM) approach coupled with stable isotope labeling and low mass resolution-triple quadrupole mass spectrometry. In the present work, we further demonstrate an accurate quantification method using a high-resolution, accurate-mass Orbitrap mass spectrometer for the measurement of the covalent linkage between 2'-deoxyguanosine (dG) and cysteine (Cys), specifically termed dG-Me-Cys, one kind of linkages derived from the formaldehyde-induced DPCs. This quantification method with a wide dynamic range of at least 3 orders generates an interference-free spectrum for unbiased and unambiguous quantification, resulting in good intra- and interday precisions and accuracies with less than 10% variations. The endogenous and exogenous amounts of dG-Me-Cys in a human cell line treated with formaldehyde are analyzed by our new methodology. The quantification strategy demonstrated in this study can be widely applied to characterize and quantify other DPC linkages induced by formaldehyde or other chemical agents.