Differential Gel-Based Proteomic Approach for Cancer Biomarker Discovery Using Human Plasma

  • Keun Na
  • Min-Jung Lee
  • Hye-Jin Jeong
  • Hoguen Kim
  • Young-Ki PaikEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 854)


Two-dimensional fluorescence difference gel electrophoresis (2D DIGE) has become a general platform for analysis of various clinical samples such as biofluids and tissues. In comparison to conventional 2-D polyacrylamide gel electrophoresis (2D PAGE), 2D DIGE offers several advantages, such as accuracy and reproducibility between experiments, which facilitate spot-to-spot comparisons. Although whole plasma can be easily obtained, the complexity of plasma samples makes it challenging to analyze samples with good reproducibility. Here, we describe a method for decreasing protein complexity in plasma samples within a narrow pH range by depleting high-abundance plasma proteins. In combination with analysis of differentially expressed spots, trypsin digestion, identification of protein by mass spectrometry, and standard 2D PAGE and DIGE, this method has been optimized for comparison of plasma samples from healthy donors and patients diagnosed with hepatocellular carcinoma.

Key words

Two-dimensional fluorescence difference gel electrophoresis Narrow pH range Plasma proteomics Hepatocellular carcinoma Biomarker 



This study was supported by a grant from the National R&D Program for Cancer Control (1120200 to YKP), National Project for the Personalized Medicine, Ministry for Health and Welfare, Republic of Korea (A111218-11-CP01 to YKP). The authors declare no conflicts of interest. Corresponding author: Young-Ki Paik (


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Keun Na
    • 1
  • Min-Jung Lee
    • 2
  • Hye-Jin Jeong
    • 3
  • Hoguen Kim
    • 4
  • Young-Ki Paik
    • 5
    Email author
  1. 1.Graduate Program in Functional GenomicsYonsei UniversitySeoulSouth Korea
  2. 2.Integrated OMICS for Biomedical ScienceYonsei UniversitySeoulSouth Korea
  3. 3.Yonsei Proteome Research CenterYonsei UniversitySeoulSouth Korea
  4. 4.Department of PathologyYonsei University College of MedicineSeoulSouth Korea
  5. 5.Department of BiochemistryYonsei UniversitySeoulSouth Korea

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