Top-Down Mass Spectrometry for Sequencing of Larger (up to 61 nt) RNA by CAD and EDD

We have studied the effect of solution additives on hydrolysis and charge state distribution in ESI MS of RNA. Lower and higher charge state ions can be electrosprayed from solutions containing 25 mM piperidine/25 mM imidazole and 1% vol. triethylamine, respectively, with base-catalyzed hydrolysis rates that are sufficiently slow to perform MS/MS experiments. These lower and higher charge state ions are suitable as precursors for CAD and EDD, respectively. We demonstrate nearly complete sequence coverage for 61 nt RNA dissociated by CAD, and 34 nt RNA dissociated by EDD, and suggest a mechanism for backbone fragmentation in EDD of RNA.

Graphical AbstractExtensive sequence coverage from CAD and EDD of 61 nt RNA is demonstrated, and a mechanism for EDD backbone cleavage proposed.Figure optionsDownload full-size imageDownload high-quality image (44 K)Download as PowerPoint slide