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Improved application of RNAModMapper – An RNA modification mapping software tool – For analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data

Lobue, Peter A., Yu, Ningxi, Jora, Manasses, Abernathy, Scott, Limbach, Patrick A.
Methods 2019 v.156 pp. 128-138
RNA, computer software, data collection, gene expression regulation, liquid chromatography, tandem mass spectrometry
Research into post-transcriptional processing and modification of RNA continues to speed forward, as their ever-emerging role in the regulation of gene expression in biological systems continues to unravel. Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven for over two decades to be a powerful ally in the elucidation of RNA modification identity and location, but the technique has not proceeded without its own unique technical challenges. The throughput of LC-MS/MS modification mapping experiments continues to be impeded by tedious and time-consuming spectral interpretation, particularly during for the analysis of complex RNA samples. RNAModMapper was recently developed as a tool to improve the interpretation and annotation of LC-MS/MS data sets from samples containing post-transcriptionally modified RNAs. Here, we delve deeper into the methodology and practice of RNAModMapper to provide greater insight into its utility, and remaining hurdles, in current RNA modification mapping experiments.