RNabelA Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids

The past decade has witnessed a surging demand for accurate identification and localization of RNA modifications in both endogenous and synthetic therapeutic RNAs. With accurate spectral annotation for RNA, tandem mass spectrometry (MS/MS) can meet this demand.

Here, we present RNabel, a user-friendly software tool for in-depth annotation of MS/MS spectra of RNA oligonucleotides. RNabel considers a full set of backbone-cleavage ions (<i>a</i>, <i>b</i>, <i>c</i>, <i>d</i>, <i>a-B</i>, <i>w</i>, <i>x</i>, <i>y</i>, <i>z</i>) in which the ribonucleotide unit could be A, U, C, G, Y (pseudouridine), or I (Inosine). Additionally, RNabel considers 196 modifications on the base, the phosphoribose linkage, the 5′ or the 3′ terminus, or the detachment of a subnucleotide fragment as a neutral or charged group.