A novel software has been created to comprehensively characterize covalent modifications of DNA through mass spectral analysis of enzymatically hydrolyzed DNA using the neutral loss of 2′-deoxyribose, a nearly universal MS2 fragmentation process of protonated 2′-deoxyribonucleosides. These covalent modifications termed DNA adducts form through xenobiotic exposures or by reaction with endogenous electrophiles and can induce mutations during cell division and initiate carcinogenesis. DNA adducts are typically present at trace levels in the human genome, requiring a very sensitive and comprehensive data acquisition and analysis method. Our software, wSIM-City, was created to process mass spectral data acquired by a wide selected ion monitoring (wSIM) with gas-phase fractionation and coupled to wide MS2 fragmentation. This untargeted approach can detect DNA adducts at trace levels as low as 1.5 adducts per 109 nucleotides. This level of sensitivity is sufficient for comprehensive analysis and characterization of DNA modifications in human specimens.
Bibliographical noteFunding Information:
This work was supported by the University of Minnesota Masonic Cancer Center, the National Cancer Institute (R01CA122320, R01CA220367, and R50CA211256), and the National Institute of Environmental Health Sciences (R01ES019564, U2CES026533, and R03ES031188). Mass spectrometry was supported by Cancer Center Support Grant CA077598 from the National Cancer Institute, and human biospecimens were supported by the National Center for Advancing Translational Sciences of the National Institutes of Health award number UL1TR000114. The Turesky laboratory gratefully acknowledges the support of the Masonic Chair in Cancer Causation.
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