Uncovering unknown pathological mechanisms and body response to applied medication are the driving forces toward personalized medicine. In this post-genomic era, all eyes are turned to the proteomics field, searching for answers and explanations by investigating the gene end point functional units—proteins and their proteoforms. The development of cutting-edge mass spectrometric technologies and bioinformatics tools have allowed the life- science community to discover disease-specific proteins as biomarkers, which are often concealed by high sample complexity and dynamic range of abundance. Currently, there are several proteomics-based approaches to investigate the proteome. This chapter focuses on gold standard proteomics strategies and related issues toward candidate biomarker discovery, which may have diagnostic/ prognostic as well as mechanistic utility in cancer drug resistance.