Muscadine grapes (Vitis rotundifolia), which are native to southeast USA region are known to be potential source of antioxidant and other polyphenolic compounds, which show anticancer, anti-inflammatory, anti-arthritic activities. Since the biologically active natural products show mild or no side effects on the body in comparison to chemically synthesized drugs, it is desirable to explore natural products for their anticancer activities. In order to investigate the phenolic compound biosynthesis, we have conducted a detailed proteome profiling of berry using iTRAQ labeling followed by LC/MS analysis. Berries from selected Muscadine genotypes were collected and bioactive compounds were extracted from seed, skin and, pulp. The crude fractions were used to study bioactivity against lung and breast cancer cell lines. Active fractions were purified and each fraction was further evaluated for its bioactivity against these cell lines. Among the three tissue types tested, grape seed extract showed the highest biological activity. We also observed significant genetic diversity of biological activity among muscadine genotypes. Proteome analysis revealed more than 700 differentially expressed proteins during berry development and ripening. Various biological pathways related to active metabolite synthesis will be described in detail.