Breast cancer is the most commonly diagnosed cancer and remains the second most common cause of cancer-related deaths in women. Proteomics has been used in biomedical research for 20 years. However, the application of proteomics in breast cancer remains a small fraction of breast cancer research. Comprehensive analysis of proteins is seldom used in clinical practice. Analysis of single proteins still remains the standard practice in clinical laboratories. Despite the use of multiplex methods for protein analysis in preclinical research, it is challenging to apply these techniques in the clinical setting. In this review, we summarize the commonly implemented array-based and mass spectrometry-based proteomic techniques, and the application of biomarkers for a specific purpose or mechanisms involved in breast cancer biology. The ultimate goal of this review is to help clinicians and scientists for choosing the right techniques and understanding their potential with respect to prognosis and prediction of the treatment outcome.
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