Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry

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.