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Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry

Author

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  • Luigi D’Ascenzo

    (The Scripps Research Institute
    Genentech Inc.)

  • Anna M. Popova

    (The Scripps Research Institute)

  • Scott Abernathy

    (University of Cincinnati)

  • Kai Sheng

    (The Scripps Research Institute)

  • Patrick A. Limbach

    (University of Cincinnati)

  • James R. Williamson

    (The Scripps Research Institute)

Abstract

Mass spectrometry is an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated into RNA therapeutics. To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. The main features of Pytheas are flexible handling of isotope labeling and RNA modifications, with false discovery rate statistical validation based on sequence decoys. We demonstrate bottom-up mass spectrometry characterization of diverse RNA sequences, with broad applications in the biology of stable RNAs, and quality control of RNA therapeutics and mRNA vaccines.

Suggested Citation

  • Luigi D’Ascenzo & Anna M. Popova & Scott Abernathy & Kai Sheng & Patrick A. Limbach & James R. Williamson, 2022. "Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30057-5
    DOI: 10.1038/s41467-022-30057-5
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