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Submitted on December 12, 2003
Revised on January 12, 2004
Accepted on January 15, 2004

Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry

Chen Li, Yi Hong, Ye Xiong Tan, Hu Zhou, Jian Hua Ai, Su Jun Li, Lei Zhang, Qi Chang Xia, Jia Rui Wu, Hong Yang Wang, and Rong Zeng

Research Center for Proteome Analysis, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031

Corresponding Author: zr{at}sibs.ac.cn

Laser capture microdissection (LCM) is a powerful tool that enables the isolation of specific cell types from tissue sections, overcoming the problem of tissue heterogeneity and contamination. This study combined the LCM with isotope-coded affinity tag technology and two-dimensional liquid chromatography to investigate the qualitative and quantitative proteomes of hepatocellular carcinoma (HCC). The effects of three different histochemical stains on tissue sections have been compared and toluidine blue stain was proved as the most suitable stain for laser capture microdissection followed by proteomic analysis. The solubilized proteins from microdissected HCC and non-HCC hepatocytes were qualitatively and quantitatively analyzed with two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) alone or coupled with cleavable isotope-coded affinity tag (cICAT) labeling technology. A total of 644 proteins were qualitative identified and 261 proteins were unambiguously quantified. These results showed that the clinical proteomic method using LCM coupled with ICAT and 2D-LC-MS/MS can carry out not only large-scale but also accurate qualitative and quantitative analysis.


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