Open-source liquid chromatography-mass spectrometry data processing tools for RNA modification analysis

RNA modifications have attracted increasing attention due to their importance in biological functions and the development of RNA therapeutics. Over the past decades, >170 biochemical modifications of RNA have been identified, which play physiological and pathological roles. Besides those naturally occurring modifications, synthetic chemical modifications are important to RNA-based therapeutics. Currently, liquid chromatography-mass spectrometry (LC-MS) stands as the critical technique capable of directly and comprehensively characterizing a large variety of chemical modifications in RNAs. However, the reliance on commercial software for LC-MS data processing can restrict accessibility, flexibility, and customization for researchers. Open-source tools provide a valuable alternative by offering cost-effective, transparent, and adaptable solutions. In this review, we examine LC-MS methodologies and open-source data processing tools for RNA modification analysis, highlighting their strengths, limitations, and suitability for specific research applications. We also discuss future advancements in LC-MS approaches, including the integration of artificial intelligence and machine learning to enhance data analysis.