Mass spectrometry (Tokyo, Japan)Jul 13, 2026

Using the Peptide Barcode Method to Quickly Screen mRNA Control Sequences

mRNA Technology Weekly Brief ↗PubMed ↗DOI ↗

Updated Jul 14, 2026

Abstract

A multiplexed evaluation method using peptide barcodes can distinguish and quantify protein expression from multiple mRNA candidates within a single sample.

Incorporating regulatory sequences can enhance cell-type-specific targeting for mRNA therapeutics.
Conventional screening methods for optimizing these sequences are extensive and time-consuming.
The new methodology demonstrated equivalent results to individual evaluations while requiring fewer samples.
Simultaneous co-transfections allow for more efficient screening of mRNA expression control sequences.
This approach may accelerate the development of mRNA therapeutics with improved targeting specificity.

Simplified

The precise control of specific protein expression in target cells remains a critical challenge for the advancement of messenger RNA (mRNA) therapeutics. While incorporating regulatory sequences, such as microRNA-responsive RNA switches, is a promising approach for cell-type-specific targeting, optimizing these sequences requires extensive and time-consuming screening using conventional evaluation methods. In this study, we applied a multiplexed evaluation methodology utilizing peptide barcodes coupled with liquid chromatography-mass spectrometry (LC-MS) to improve the screening and design efficiency of mRNA expression control sequences. We designed mRNAs equipped with cell-specific expression control sequences and fused unique peptide barcodes to the encoded target proteins. By comparing conventional individual transfections with simultaneous co-transfections, we demonstrated that our LC-MS-based method can successfully distinguish and quantify protein expression derived from individual mRNA candidates within a single mixed sample. The simultaneous evaluation using peptide barcodes yielded results equivalent to the individual evaluations but required a reduced number of samples. This multiplexed technology would accelerate the screening process for regulatory sequences and is expected to enhance the development of mRNA therapeutics with high targeting specificity.

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Using the Peptide Barcode Method to Quickly Screen mRNA Control Sequences

Abstract

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