Related Experiment Video
Updated: Oct 25, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
Published on: September 28, 2017
RNabel─A Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids
Ge Song1,2, Yi-Jie Nathan Du3, Rui-Xiang Sun2,4
1Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences , Beijing100730, China.
Abstract:
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 (a, b, c, d, a-B, w, x, y, z) 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.
More Related Videos
08:00Sample Preparation and Relative Quantitation using Reductive Methylation of Amines for Peptidomics Studies
Published on: November 4, 2021
05:412D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
Published on: July 10, 2020
Related Concept Videos
Tandem Mass Spectrometry
Peptide Identification Using Tandem Mass Spectrometry
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
MALDI-TOF Mass Spectrometry