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Comparative Analysis of Ribonucleic Acid Digests (CARD) by Mass Spectrometry

  • Mellie June Paulines
  • Patrick A. LimbachEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1562)

Abstract

We describe the comparative analysis of ribonucleic acid digests (CARD) approach for RNA modification analysis. This approach employs isotope labeling during RNase digestion, which allows the direct comparison of a tRNA of unknown modification status against a reference tRNA, whose sequence or modification status is known. The reference sample is labeled with 18O during RNase digestion while the candidate (unknown) sample is labeled with 16O. These RNase digestion products are combined and analyzed by mass spectrometry. Identical RNase digestion products will appear in the mass spectrum as characteristic doublets, separated by 2 Da due to the 16O/18O mass difference. Singlets arise in the mass spectrum when the sequence or modification status of a particular RNase digestion product from the reference is not matched in the candidate (unknown) sample. This CARD approach for RNA modification analysis simplifies the determination of differences between reference and candidate samples, providing a route for higher throughput screening of samples for modification profiles, including determination of tRNA methylation patterns.

Key words

Modified nucleosides RNA sequencing tRNA rRNA Modified bases Tandem mass spectrometry LC-MS/MS MALDI-MS/MS Isotope labeling Epitranscriptome 

Notes

Acknowledgments

Financial support of this work was provided by the National Science Foundation (CHE1507357) and the University of Cincinnati.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Rieveschl Laboratories for Mass Spectrometry, Department of ChemistryUniversity of CincinnatiCincinnatiUSA

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