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Related Experiment Video

Updated: Apr 30, 2026

Detection of Protein Ubiquitination
09:00

Detection of Protein Ubiquitination

Published on: August 19, 2009

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A COFRADIC protocol to study protein ubiquitination.

Elisabeth Stes1, Mathias Laga, Alan Walton

  • 1Department of Medical Protein Research, VIB , B-9000 Ghent, Belgium.

Journal of Proteome Research
|May 13, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for identifying ubiquitination sites using COmbined FRActional DIagonal Chromatography (COFRADIC). The technique efficiently enriches ubiquitinated peptides from cell lysates, revealing thousands of endogenous ubiquitination sites.

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Area of Science:

  • Biochemistry
  • Proteomics
  • Molecular Biology

Background:

  • Ubiquitination is a crucial post-translational modification regulating numerous cellular processes.
  • Identifying ubiquitination sites is essential for understanding protein function and cellular signaling.
  • Existing methods often require overexpression or lack specificity.

Purpose of the Study:

  • To develop and validate a novel technology for enriching ubiquitinated peptides.
  • To identify endogenous ubiquitination sites without relying on tagged ubiquitin or antibodies.
  • To characterize the ubiquitination landscape in a native human cell lysate.

Main Methods:

  • Application of COmbined FRActional DIagonal Chromatography (COFRADIC) for peptide enrichment.
  • Chemical acetylation of primary amino groups followed by specific cleavage of ubiquitin chains by USP2 catalytic core domain (USP2cc).
  • Mass spectrometry-based identification of modified peptides and ubiquitination sites.

Main Results:

  • Successful enrichment of ubiquitinated peptides.
  • Identification of over 7500 endogenous ubiquitination sites.
  • Characterization of ubiquitination in more than 3300 proteins from a human Jurkat cell lysate.

Conclusions:

  • The developed COFRADIC-based method is effective for unbiased identification of ubiquitination sites.
  • This technology bypasses limitations of previous methods, enabling deep proteome-wide ubiquitination analysis.
  • Provides a valuable tool for studying the ubiquitination landscape in native biological systems.