2026-10-12T12:09:21Z
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oai:figshare.com:article/34008981
2026-09-28T05:18:16Z
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RNabelA
Standalone Software Tool for Annotating
Tandem Mass Spectra of Modified Ribonucleic Acids
Ge Song (1754242)
Yi-Jie Nathan Du (25119606)
Rui-Xiang Sun (1797622)
Meng-Qiu Dong (154258)
Biophysics
Biochemistry
Space Science
Physical Sciences not elsewhere classified
Medicine
Molecular Biology
Pharmacology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Inorganic Chemistry
Science Policy
tandem mass spectrometry
synthetic therapeutic rnas
standalone software tool
play diverse roles
multiple statistical metrics
made freely available
https :// github
friendly software tool
create new components
cleavage ions (<
170 identified types
3 ′ terminus
rnabel batch files
ribonucleotide unit could
accurate spectral annotation
spectral annotation
could detach
accurate identification
5 ′
depth annotation
subnucleotide fragment
quality assessment
pseudouridine ),
phosphoribose linkage
past decade
inosine ).
including ribonucleotides
full set
charged groups
charged group
cellular processes
Ribonucleic
acid (RNA) modifications, with over 170 identified
types, play diverse roles in cellular processes. 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. Users can create new components if
needed, including ribonucleotides, modifications, and neutral or charged
groups that could detach from a ribonucleotide. RNabel efficiently
processes large data sets in four acceptable formats including .mgf,
.raw, .txt from msConvert, and RNabel batch files. Multiple statistical
metrics are provided for quality assessment of spectral annotation.
To accelerate RNA modification analysis, RNabel is made freely available
for Mac and Windows users at https://github.com/songge1111/RNabel/releases.
2026-09-28T00:00:00Z
Dataset
Dataset
10.1021/acs.analchem.6c02176.s002
https://figshare.com/articles/dataset/RNabel_A_Standalone_Software_Tool_for_Annotating_Tandem_Mass_Spectra_of_Modified_Ribonucleic_Acids/34008981
CC BY-NC 4.0