Protocol for preparation and measurement of intracellular and extracellular modified RNA using liquid chromatography-mass spectrometry

STAR Protoc. 2021 Sep 27;2(4):100848. doi: 10.1016/j.xpro.2021.100848. eCollection 2021 Dec 17.


About 150 modifications have been identified in RNA species. Besides their regulatory roles in the intracellular gene expression, abundant modified RNA nucleosides are catabolized from RNA and released into extracellular fluids, which can impact extracellular signaling as ligands for receptors. Here, we describe a protocol to prepare samples from biological specimens, including cultured cells, extracellular fluid, and tissues, to measure both intracellular and extracellular RNA modifications using mass spectrometry. For complete details on the use and execution of this protocol, please refer to Ogawa et al. (2021).

Keywords: Mass Spectrometry; Metabolism; Metabolomics; Molecular Biology; Signal Transduction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cells, Cultured
  • Chromatography, Liquid / methods
  • Mass Spectrometry / methods
  • Nucleosides* / analysis
  • RNA* / genetics


  • Nucleosides
  • RNA