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Updated: Jun 24, 2026
Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
Published on: February 27, 2015
Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry
Sara Zanivan1, Florian Gnad, Sara A Wickström
1Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
Abstract:
Kinases play a prominent role in tumor development, pointing to the presence of specific phosphorylation patterns in tumor tissues. Here, we investigate whether recently developed high resolution mass spectrometric (MS) methods for proteome and phosphoproteome analysis can also be applied to solid tumors. As tumor model, we used TG3 mutant mice carrying skin melanomas. At total of 100 microg of solid tumor lysate yielded a melanoma proteome of 4443 identified proteins, including at least 88 putative melanoma markers previously found by cDNA microarray technology. Analysis of 2 mg of lysate from dissected melanoma with titansphere chromatography and 8 mg with strong cation exchange together resulted in the identification of more than 5600 phosphorylation sites on 2250 proteins. The phosphoproteome included many hits from pathways important in melanoma. One-month storage at -80 degrees C did not significantly decrease the number of identified phosphorylation sites. Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies.
Insights
High-resolution mass spectrometry (MS) successfully analyzes melanoma proteomes and phosphoproteomes from solid tumors. This method is efficient, even with small biopsy amounts, aiding cancer research.
Area of Science:
- Proteomics and Phosphoproteomics
- Cancer Research
- Mass Spectrometry (MS) Applications
Background:
- Kinases are crucial in tumor development, indicated by distinct phosphorylation patterns in tumor tissues.
- Existing high-resolution mass spectrometry (MS) methods are effective for cell cultures but their application to solid tumors is less explored.
Purpose of the Study:
- To investigate the applicability of advanced high-resolution MS for proteome and phosphoproteome analysis in solid tumors.
- To assess the efficiency of MS-based proteomics on limited solid tumor samples, comparable to cell culture models.
Main Methods:
- Utilized TG3 mutant mice with skin melanomas as a solid tumor model.
- Employed high-resolution mass spectrometry (MS) for proteome and phosphoproteome analysis.
- Applied titansphere chromatography and strong cation exchange for phosphoproteome enrichment and analysis.
Main Results:
- Identified 4443 proteins in 100 microg of melanoma lysate, including 88 melanoma markers.
- Discovered over 5600 phosphorylation sites on 2250 proteins from 2 mg and 8 mg of melanoma lysate.
- Found that one-month storage at -80°C did not significantly impact the identification of phosphorylation sites.
Conclusions:
- High-resolution MS-based proteomics is effective for analyzing solid tumors, comparable to cell culture models.
- The methodology is efficient with sample amounts compatible with clinical biopsies.
- This approach facilitates the study of melanoma pathways and markers through proteome and phosphoproteome analysis.
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