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Native Charge Detection Mass Spectrometry of Kilobase-Scale Messenger RNAs
Raihana Afroz1, Kyle P Bowen2, Weijing Liu2
1Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.
Analytical Chemistry
|May 22, 2026
Summary
Charge detection mass spectrometry (CDMS) accurately measures the mass and charge of intact messenger RNAs (mRNAs). This method identifies impurities and provides insights into RNA structure, aiding RNA biotherapeutic development.
Area of Science:
- Analytical Chemistry
- Biochemistry
- Molecular Biology
Background:
- Conventional mass spectrometry struggles with large, heterogeneous biomolecules like messenger RNAs (mRNAs).
- Messenger RNAs are challenging due to their size, heterogeneity, and tendency to form oligomers.
- Existing workflows limit the assessment of intact mRNA structure and purity.
Purpose of the Study:
- To optimize and evaluate native Charge Detection Mass Spectrometry (CDMS) for intact analysis of long messenger RNAs.
- To compare positive and negative analysis polarities for messenger RNA characterization.
- To establish CDMS as a versatile platform for RNA biotherapeutic development.
Main Methods:
- Optimization and evaluation of native CDMS for intact messenger RNA analysis.
- Systematic comparison of positive and negative ion polarities.
- Use of collisional activation to improve mass accuracy and impurity resolution.
Main Results:
- Native CDMS enables direct and accurate mass measurement of intact messenger RNAs (1,000–4,500 nucleotides).
- The method detects process-related impurities like truncations and dimers.
- Charge distributions correlate with transcript length and respond predictably to experimental conditions.
- Negative polarity generally yields higher charge states, improving sensitivity and size discrimination.
Conclusions:
- Native CDMS is a versatile platform for intact mRNA characterization.
- The technique provides simultaneous mass, charge, and impurity information.
- CDMS complements existing methods and supports RNA biotherapeutic development.
