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IsoPS-DIA: Dual Functionality of Absolute Targeted Quantification and Global Proteome Profiling.

Hsin-Ju Chan1,2, Huan-Chi Chiu1,2, Li-Yu Chen1,2

  • 1Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.

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Summary
This summary is machine-generated.

This study introduces IsoPS-DIA, a new method for precisely measuring mutant proteins and their signaling pathways. It bridges genetic mutations and protein expression for better precision oncology.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Cancer Genomics

Background:

  • Gene testing alone is insufficient for cancer drug targeting, as it misses protein expression levels.
  • Comprehensive evaluation requires integrated methods for mutant protein quantification and pathway analysis.

Purpose of the Study:

  • To develop and validate a novel mass spectrometry strategy, IsoPS-DIA, for absolute quantification of mutant proteins and global proteome profiling.
  • To demonstrate the method's utility in analyzing EGFR and KRAS mutations in lung cancer cell lines.

Main Methods:

  • Developed an isotope pair-separated data-independent acquisition (IsoPS-DIA) strategy with a dual-window design.
  • Applied IsoPS-DIA to lung cancer cell lines with EGFR mutations (L858R, G719A, Del19).
  • Benchmarked IsoPS-DIA against PRM, Fix-DIA, and Var-DIA.

Main Results:

  • Achieved subfemtomole sensitivity, excellent linearity (R^2=0.998-0.999), and high reproducibility (CV ~3%).
  • Quantified endogenous EGFR and KRAS mutations alongside wild-type proteins, revealing allele-specific expression.
  • Profiled >6,000 proteins, uncovering signaling variability and actionable variants like KRAS-G12S.

Conclusions:

  • IsoPS-DIA effectively bridges genotype and proteotype by precisely quantifying mutant proteins and global proteomes.
  • The method offers a scalable, reproducible platform for precision oncology, improving upon existing genomic analyses.
  • IsoPS-DIA demonstrates superior accuracy and reproducibility compared to other DIA methods without sacrificing proteome coverage.