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Label-free quantitative proteomics of CD133-positive liver cancer stem cells

Sheng-Ta Tsai12, Chih-Chiang Tsou3, Wan-Yu Mao2, Wei-Chao Chang2, Hsin-Ying Han2, Wen-Lian Hsu3, Chung-Leung Li24, Chia-Ning Shen12* and Chung-Hsuan Chen1256*

Author Affiliations

1 Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, Taiwan

2 Genomics Research Center, Academia Sinica, Taipei, Taiwan

3 Institute of Information Science, Academia Sinica, Taipei, Taiwan

4 Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan

5 Department of Chemistry, National Taiwan University, Taipei, Taiwan

6 Institute of Atomic & Molecular Sciences, Academia Sinica, Taipei, Taiwan

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Proteome Science 2012, 10:69  doi:10.1186/1477-5956-10-69

Published: 21 November 2012



CD133-positive liver cancer stem cells, which are characterized by their resistance to conventional chemotherapy and their tumor initiation ability at limited dilutions, have been recognized as a critical target in liver cancer therapeutics. In the current work, we developed a label-free quantitative method to investigate the proteome of CD133-positive liver cancer stem cells for the purpose of identifying unique biomarkers that can be utilized for targeting liver cancer stem cells. Label-free quantitation was performed in combination with ID-based Elution time Alignment by Linear regression Quantitation (IDEAL-Q) and MaxQuant.


Initially, IDEAL-Q analysis revealed that 151 proteins were differentially expressed in the CD133-positive hepatoma cells when compared with CD133-negative cells. We then analyzed these 151 differentially expressed proteins by MaxQuant software and identified 10 significantly up-regulated proteins. The results were further validated by RT-PCR, western blot, flow cytometry or immunofluorescent staining which revealed that prominin-1, annexin A1, annexin A3, transgelin, creatine kinase B, vimentin, and EpCAM were indeed highly expressed in the CD133-positive hepatoma cells.


These findings confirmed that mass spectrometry-based label-free quantitative proteomics can be used to gain insights into liver cancer stem cells.

Hepatocellular carcinoma; LC-MS/MS; Liver cancer stem cells; Label-free quantitation