Proteomics, the comprehensive analysis of a protein complement in a cell, tissue or biological fluid at a given time, has been enabled by quantum leaps in mass spectrometric technology, which allowed identification of large, involatile biomolecules. Over the last two decades, this discipline evolved from the sole delivery of protein identities to a platform, which reveals clues to function through e.g. characterisation of protein modifications and interactions as well as through quantitative proteomics, i.e. the global comparison of protein amounts between two defined biological states. Proteomics is an integral part and key player in the family of -omic disciplines as there are genomics (gene analysis), transcriptomics (gene expression analysis) and metabolomics (metabolite profiling). Considering the complexity, dynamics and protein concentration range of any given proteome, proteomics is the most challenging -omic discipline and requires the most sophisticated analysis pipeline. Proteomics represents an established technology in the pharmaceutical industry mainly for biomarker and drug target discovery. The potential of proteomics for research in the food industry is increasingly being recognised and the employment of proteomic approaches to nutrition and health issues is now emerging. This review summarizes (i) major technological achievements in mass spectrometry and proteomics, (ii) deliverables of proteomics in the context of nutrition and health, and (iii) applications of proteomics, and - if appropriate transcriptomics to the research fields of digestive health, obesity and diabetes, immunity and allergy, probiotics, milk, and food preference.