A Highly Sensitive and High-Throughput Quantitative HILIC-MS/MS Method for Systematic Profiling of RNA Modifications

Understanding the functions and regulatory mechanisms of the epitranscriptome entails robust and accurate analytical methods to identify and quantify post-transcriptional modifications in RNA. However, there are still various challenges in analyzing multiple modified nucleosides in RNA. Herein, we established a highly sensitive and high-throughput hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method, in conjunction with a stable isotope-dilution technique, for accurate quantification of 35 nucleosides. By the use of malic acid as a mobile phase additive, the HILIC-based separation of nucleosides was improved and the MS signal response of nucleosides was enhanced by 2.5- to 20.0-fold. Notably, seven groups of isomeric nucleosides with identical multiple-reaction monitoring ion transitions and six groups of nucleosides with identical or similar molecular weights that were indistinguishable by MS were well resolved by optimal HILIC separation. Thirty-five nucleosides were analyzed simultaneously within 12.5 min, and the limits of detection of these nucleosides ranged from 15.0 amol to 43.5 fmol. With this method, we conducted a comprehensive analysis and evaluation of the alteration in the RNA modification profile in breast cancer and assessed the RNA modification patterns across different breast cancer subtypes. The developed HILIC-MS/MS method has excellent capabilities for sensitive and high-throughput detection of multiple modified nucleosides, thereby providing a valuable analytical tool for deciphering the epitranscriptomic landscape and screening nucleosides as biomarkers in future clinical research.