Determining the role of diets in metabolic control and improving health is a central scientific goal of food science. In the post-genome age, there are several significant challenges and risks for nutrition research. New omics technologies and bioinformatic methods provide tremendous potential for exploring the dynamic relationship between metabolism and nutrition. This paper, which emphasizes advanced nutrition proteomics, nutriproteomics, and nutrimetabolomics in nutrition science, provides an overview of omics technologies in human nutrition. There is also a discussion of the current limitations and possible opportunities. Combining different omics technologies, systems biology would make the development of new genetic markers correlated with particular nutrients or other nutritional factors much more accessible. Future human nutrition studies focused on omics can be anticipated to include tailored dietary guidelines for preventative medicine.