There are approximately 100,000 proteins in humans with various physiological functions. The complement of proteins in the organism as well as their interactions is defined as the proteome. Its analysis (proteomics) by highly specific, sensitive, and accurate MS has been made possible with matrix-assisted laser desorption ionization or electrospray ionization of proteins and large peptides. Currently, the most commonly used proteomics technologies involve either specific digestion of proteins (the bottom-up approach using 2-dimensional polyacrylamide gel electrophoresis and multidimensional protein identification technology) or direct analysis of intact proteins after their chromatographic separation (the top-down approach and surface-enhanced laser desorption ionization). Proteomics holds great promise for discoveries in nutrition research, including profiles and characteristics of dietary and body proteins; digestion, absorption, and metabolism of nutrients; functions of nutrients and other dietary factors in growth, reproduction, and health; biomarkers of the nutritional status and disease; and individualized requirements of nutrients. The proteome analysis is expected to play an important role in solving major nutrition-associated problems in humans and animals, such as obesity, diabetes, cardiovascular disease, cancer, aging, and intrauterine fetal retardation.