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Related Experiment Video

Updated: May 6, 2026

Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling
11:53

Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling

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Mass defect-based pseudo-isobaric dimethyl labeling for proteome quantification.

Yuan Zhou1, Yichu Shan, Qi Wu

  • 1National Chromatographic Research and Analysis Center, Key Lab of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, China.

Analytical Chemistry
|November 5, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a new proteome quantification method, pseudo-isobaric dimethyl labeling (pIDL), for accurate and precise protein analysis. The pIDL method offers a wide dynamic range and was successfully applied to study mouse cancer cell lines.

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Last Updated: May 6, 2026

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Accurate proteome quantification is crucial for understanding biological processes and disease.
  • Existing methods often face limitations in accuracy, precision, or dynamic range.

Purpose of the Study:

  • To develop a novel, highly accurate, and precise mass spectrometry-based proteome quantification method.
  • To establish a pseudo-isobaric dimethyl labeling (pIDL) technique utilizing mass defect differences.
  • To apply the pIDL method for comparative proteomic analysis of distinct biological samples.

Main Methods:

  • Development of a mass defect-based pseudo-isobaric dimethyl labeling (pIDL) strategy.
  • Utilizing subtle mass defect differences between (12)C/(13)C and (1)H/(2)H isotopes for labeling.
  • Employing Lys-C protein digests labeled with CD2O/(13)CD2O and reduced with NaCNBD3/NaCNBH3.
  • High-resolution tandem mass spectrometry (MS/MS) for resolving fragment ion pairs and quantification.

Main Results:

  • The pIDL method achieved highly accurate and precise proteome quantification.
  • Demonstrated a dynamic range of approximately 100-fold.
  • Successfully extended the pIDL method to 4-plex proteome quantification.
  • Applied pIDL to analyze differential proteomes of mouse hepatocarcinoma cell lines (Hca-P and Hca-F) with varying metastatic potential.

Conclusions:

  • The mass defect-based pIDL method provides a robust approach for accurate and precise proteome quantification.
  • pIDL offers a significant improvement in dynamic range compared to existing methods.
  • This technique is valuable for comparative proteomic studies, including the analysis of cancer cell line differences in metastasis.