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Sensitive and Accurate Proteome Profiling of Embryogenesis Using Real-Time Search and TMTproC Quantification.

Alex N T Johnson1, Jingjing Huang2, Argit Marishta3

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Summary

This study introduces TMTproC-RTS, a new method enhancing multiplexed proteomics sensitivity and accuracy. It enables deeper quantification of protein dynamics in early embryogenesis across multiple species.

Keywords:
Ciona robustaDrosophila melanogasterTMTproXenopus laeviscomplementary ion quantificationmultiplexing

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Area of Science:

  • Proteomics
  • Systems Biology
  • Developmental Biology

Background:

  • Multiplexed proteomics is vital for biological system investigation.
  • TMTproC complementary ions address ratio distortion but require long acquisition times.
  • Real-time search (RTS) algorithms improve speed and sensitivity in proteomics.

Purpose of the Study:

  • To combine TMTproC complementary ion quantification with RTS (TMTproC-RTS).
  • To enhance sensitivity, accuracy, and precision in MS2-level quantitative proteomics.
  • To analyze protein dynamics during early embryogenesis in diverse model organisms.

Main Methods:

  • Integration of TMTproC complementary ion quantification with real-time search (RTS).
  • Application of the TMTproC-RTS method to quantify protein dynamics in embryonic development.
  • Utilizing Orbitrap mass spectrometry for high-resolution quantitative analysis.

Main Results:

  • Demonstrated enhanced sensitivity and accuracy in MS2-level quantitative proteomics.
  • Quantified 7.8k (fly), 8.6k (sea squirt), and 12.7k (frog) proteins, a 12-14% improvement over naive TMTproC.
  • Generated deep and accurate protein dynamics datasets for three model organisms.

Conclusions:

  • TMTproC-RTS significantly improves protein quantification in multiplexed proteomics.
  • The method provides valuable insights into evolutionary comparisons of early embryogenesis.
  • This work establishes a robust dataset for studying developmental protein dynamics.