Proteomics, the study of entire compendium of proteins encoded by a genome, is now established as a leading technological platform for numerous areas of clinical research in personalized medicine: understanding of disease pathogenesis, detection of disease specific biomarkers and identification of novel drug and vaccine targets, to name a few. The successful integration of nanotechnology with proteomics has introduced a novel hybrid analytical platform known as “nanoproteomics”. Recent advances in the field of nanoproteomics have introduced nano-based approaches into personalized medicine and targeted therapeutics. Amongst the miscellaneous promising candidates, quantum particles, carbon nanotubes and nanowires, nanoscopic gold particles are promising for diagnostic and therapeutic applications due to their high sensitivity, versatile dynamic range, real-time monitoring power, multiplexing and high-throughput capability. Personalized medicine and targeted therapeutics are rapidly advancing frontiers of healthcare that is informed by the individual persons unique clinical, genetic, genomic, proteomic and environmental information. This paper synthesizes the promising applications of nanoproteomic technologies in context of personalized medicine and molecular therapeutics as well as its impacts on clinical research. Finally, we share our recent experience in employing nanoproteomics technology platforms in India. We provide an outlook of why proteomics-based approaches might offer unique and complementary advantages in personalized medicine R&D that has hitherto relied to a large extent on genomics technology platforms. We conclude that genomics and nanoproteomics, when used in combination, can be a powerful approach that can propel personalized healthcare from the discovery lab to clinic and global public health practice.