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Updated: Feb 18, 2026

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Programmable Multiplexed Proteomics via Sequence-Encoded Mass Tagging.

Xinyi Sun1,2, Haoni Yan1, Aiting Wang1,2

  • 1Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.

Analytical Chemistry
|February 16, 2026
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Summary
This summary is machine-generated.

Introducing ePAS, an isotope-free tagging strategy for proteomics. This novel method uses sequence-defined chemical modules, overcoming limitations of traditional isotopic tags for scalable, cost-effective, and high-throughput analysis.

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biotechnology

Background:

  • Isobaric tagging revolutionized proteomics quantification but faces limitations in scalability, synthesis complexity, and cost due to isotopic encoding.
  • Existing methods hinder ultrahigh-throughput applications in clinical and single-cell research.

Purpose of the Study:

  • Introduce ePAS (expandable Platform by Arrangement of Sequence), a novel isotope-free tagging strategy for proteomics.
  • Overcome the intrinsic limitations of isotopic tags for enhanced scalability, synthesis, and cost-effectiveness.

Main Methods:

  • Developed ePAS, utilizing sequence-defined chemical modules and noncanonical amino acids (ncAAs) instead of isotopic elements.
  • Incorporated a proline-based moiety for sequence-specific reporter generation upon MS/MS fragmentation.
  • Designed and synthesized a triplex ePAS tag set for proof-of-concept studies.

Main Results:

  • Demonstrated robust performance in complex biological samples (peptides, E. coli, S. aureus lysates).
  • Achieved high labeling efficiency (>90%), accurate quantification (proportional error <20%), and broad dynamic range.
  • Showcased combinatorial growth in multiplexing capacity with increasing ncAAs.

Conclusions:

  • ePAS is a universal, synthesis-friendly, and programmable platform overcoming isotopic tag limitations.
  • This novel strategy enables ultrahigh-throughput proteomics.
  • Opens new avenues for clinical and single-cell proteomics applications.