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A method for nontargeted analysis of modified nucleotides in DNA (and RNA) is reported based on labeling with benzoylhistamine (BH) followed by MALDI-MS. The method provides deoxynucleotide-specific detection, accurate measurement of molecular ions, high sensitivity, semiquantitation, and, to the extent studied to date, normalization of response within a factor of &lt;3.

Nontargeted Nucleotide Analysis Based on Benzoylhistamine Labeling-MALDI-TOF/TOF-MS: Discovery of Putative 6-Oxo-Thymine in DNA