Quantification of Epigenetic DNA and RNA Modifications by UHPLC–MS/MS Technologies: New Concepts and New Improvements for the Special Collections

ABSTRACT Dynamic and reversible DNA and RNA modifications are essential for cell differentiation and development. Aberrant epigenetic modifications are closely associated with the occurrence and progression of diseases, serving as potential markers for cancer diagnosis and prognosis. Ultra‐high‐performance liquid chromatography coupled with tandem mass spectrometry (UHPLC–MS/MS) offers distinct advantages in the qualitative and quantitative analysis of various modifications due to its sensitivity, specificity, and accuracy. This review provides a comprehensive overview of the current knowledge regarding the liquid chromatography–mass spectrometry (LC–MS) analysis of DNA and RNA modifications, including analytical procedures, advancements, and biological applications, with a focus on tracing the source of (N6‐2′‐deoxy‐adenosine) 6mdA in eukaryotes. Additionally, we examine the integration of UHPLC–MS/MS with other separation techniques to achieve accurate quantification of modifications in specific regions, certain fragments, and free nucleosides.