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Reagents for Isobaric Labeling Peptides in Quantitative Proteomics.

Yan Ren1, Yanbin He1, Zhilong Lin1

  • 1BGI-Shenzhen , Beishan Industrial Zone 11th Building , Yantian District, Shenzhen , Guangdong 518083 , China.

Analytical Chemistry
|September 28, 2018
PubMed
Summary

We developed new, low-cost 10-plex isobaric tags (IBT) for peptide labeling, overcoming limitations of TMT and iTRAQ. These IBTs enable sensitive, quantitative proteomics with minimal bias, proving effective for phosphoproteome analysis.

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Commercial isobaric peptide labeling reagents (TMT, iTRAQ) are costly and cumbersome.
  • Quantifying modified peptides and handling variable sample sizes present experimental challenges.

Purpose of the Study:

  • To develop a novel, cost-effective 10-plex isobaric tag reagent (IBT) for peptide labeling.
  • To assess the performance of IBTs in terms of stability, labeling efficiency, dynamic range, and quantification accuracy.
  • To apply IBTs for quantitative phosphoproteomics analysis.

Main Methods:

  • Development of a 10-plex isobaric tag system (IBT).
  • Peptide labeling efficiency assessed using mass spectrometry (Orbitrap Q Exactive MS).
  • Evaluation of labeling dynamic range and quantification bias.
  • Application of IBTs for EGF-stimulated phosphoproteome analysis in HeLa cells.

Main Results:

  • IBTs demonstrated high stability and low cost compared to existing reagents.
  • Over 97% labeling efficiency was achieved with IBTs under optimized conditions.
  • A wide dynamic range of 50-fold was observed with minimal matrix effects and low quantification bias.
  • Analysis of EGF-stimulated phosphoproteome identified 5,361 unique phosphopeptides.

Conclusions:

  • IBT reagents offer a stable, cost-effective, and efficient alternative for isobaric peptide labeling.
  • IBTs provide accurate quantification and are suitable for large-scale quantitative proteomics, including phosphoproteomics.
  • The developed IBT system is a valuable tool for researchers in quantitative proteomics.