Proteomics has been widely applied to several biomedical fields in recent years. The high-throughput capability of proteomics allows simultaneous examination of numerous proteins and offers the possibility of a global analysis of proteins in cells, tissues or biofluids. The rapid progress in the field of proteomics is based primarily on the success of protein separation sciences (either gel-based or gel-free techniques) and recent advances of mass spectrometry. Unlike the genome, the proteome is dynamic and varies according to cell type and functional state of the cell. In addition, gene expression does not always correlate with protein expression as one gene can be modified to be several products or proteins that directly govern cellular function. Thus, proteome analysis is expected to provide a wealth of useful information in nutrition research on the effects of nutrients or food components on metabolic pathways. Such research allows experts to explore the regulatory mechanisms for maintaining normal homeostasis during nutritional imbalance, to better understand the pathogenic mechanisms and pathophysiology of nutritional disorders, to define molecular targets of bioactive food components and to identify biomarkers that can be used as diagnostic, predictive or prognostic factors. This paper will provide a brief overview of proteomics, a summary of current proteomic technologies and an example of proteomic application to nutrition research. Finally, the concept of systems biology, which involves integrative 'omics' (i.e., combining genomics, transcriptomics, proteomics, lipomics and metabolomics) as well as bioinformatics and modeling, will be discussed. Due to the extent of information that can be obtained from systems biology, this ideal approach holds great promise for future nutrition research.