Optimization of q Value for Sensitive Detection of Uridine and Thymidine Nucleosides by MS³

Liquid chromatography-tandem mass spectrometry has been widely used to quantify modified nucleosides enzymatically released from RNA and DNA. Compared to MS/MS, MS³ offers higher specificity for analytes in complex sample matrices because coeluting chemical interferences can be more effectively filtered out. To date, the detection of uracil- and thymine-containing nucleosides and their modified derivatives still suffers from poor sensitivity, owing, in part, to their relatively low proton affinities. In this study, we explored various settings of q values in the MS³ analysis of unmodified and chemically modified uridine and thymidine nucleosides on a linear ion trap mass spectrometer. Our results showed that increasing the q value led to markedly improved sensitivities for detecting some of these nucleosides using MS³. Our work suggests that optimizing the q value constitutes a useful approach for the highly sensitive detection of modified nucleosides and other types of analytes by MS³.