Comparative proteomic analysis of different stages of breast cancer tissues using ultra high performance liquid chromatography tandem mass spectrometer

This study investigated the proteomic profiles of different stages of breast cancer and matched adjacent normal tissues in Malaysian patients to identify potential biomarkers and protein pathways involved in carcinogenesis. The researchers collected 80 samples of tumor and adjacent normal tissues. Protein extraction was followed by separation using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Gel-Eluted Liquid Fractionation Entrapment Electrophoresis (GELFREE) Technology System to maximize protein detection. The separated protein fractions were then analyzed by tandem mass spectrometry (LC-MS/MS) using LC/MS LTQ-Orbitrap Fusion and Elite. Protein identification was performed using de novo sequencing and database matching via PEAKS software. Pathway analyses were conducted using DAVID and STRING, with molecular lists generated by the REACTOME-FI plugin. The study identified 12 proteins in stage 2 tumor tissues and 17 proteins in stage 3 tumor tissues that differed from their normal counterparts. Unique protein pathways involved in carcinogenesis within stage 2 and stage 3 breast cancers were clarified. This approach provided insights into breast cancer carcinogenesis and laid a foundation for future biomarker discoveries using differential proteomics profiling. The methodology focused on comprehensive protein identification, interaction, function, network, and signaling pathway analysis, offering valuable clues for early detection and treatment strategies.

This study investigated the proteomic profiles of different stages of breast cancer and matched adjacent normal tissues in Malaysian patients to identify potential biomarkers and protein pathways involved in carcinogenesis. The researchers collected 80 samples of tumor and adjacent normal tissues. Protein extraction was followed by separation using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Gel-Eluted Liquid Fractionation Entrapment Electrophoresis (GELFREE) Technology System to maximize protein detection. The separated protein fractions were then analyzed by tandem mass spectrometry (LC-MS/MS) using LC/MS LTQ-Orbitrap Fusion and Elite. Protein identification was performed using de novo sequencing and database matching via PEAKS software. Pathway analyses were conducted using DAVID and STRING, with molecular lists generated by the REACTOME-FI plugin. The study identified 12 proteins in stage 2 tumor tissues and 17 proteins in stage 3 tumor tissues that differed from their normal counterparts. Unique protein pathways involved in carcinogenesis within stage 2 and stage 3 breast cancers were clarified. This approach provided insights into breast cancer carcinogenesis and laid a foundation for future biomarker discoveries using differential proteomics profiling. The methodology focused on comprehensive protein identification, interaction, function, network, and signaling pathway analysis, offering valuable clues for early detection and treatment strategies. Research Background and Significance Breast cancer remains one of the most prevalent and deadly malignancies worldwide, with molecular heterogeneity posing significant challenges for early diagnosis and treatment. Proteomic profiling offers a powerful approach to unravel the complex protein