Fig. 2: RNA fragmentation and MS2 spectra matching, scoring, and visualization in Pytheas. | Nature Communications

Fig. 2: RNA fragmentation and MS2 spectra matching, scoring, and visualization in Pytheas.

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

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.

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