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. 2022 May 3;13:2424. doi: 10.1038/s41467-022-30057-5

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a McLuckey nomenclature of RNA product ions following CID fragmentation¹⁶. RNA can be cleaved at each of four bonds of the phosphodiester backbone, producing nine major fragment ion series (a/a-B/b/c/d/w/x/y/z) commonly observed in CID spectra under negative ionization. b Competing OSMs for a given precursor ion scored and ranked by Pytheas. c MS/MS spectrum of the top scoring OSM highlighted in the panel (b). d Summary table of all the predicted and matched (highlighted in color) fragment ions, with theoretically calculated m/z values. In (c) and (d) sequence-defining fragment ions are highlighted using the same color scheme as in panel (a). (c) and (d) have been rendered via Pytheas visualization tools.