Proteomics, the comprehensive analysis of a protein complement in a cell, tissue or biological fluid at a given time, is a key platform within the “omic” technologies that also encompass genomics (gene analysis), transcriptomics (gene expression analysis) and metabolomics (metabolite profiling). This review summarises protein pre-separation, identification, quantification and modification/interaction analysis and puts them into perspective for nutritional R&D. Mass spectrometry has progressed with regard to mass accuracy, resolution and protein identification performance. Separation, depletion and enrichment techniques can increasingly cope with complexity and dynamic range of proteomic samples. Hence, proteo-mic studies currently provide a broader, albeit still incomplete, coverage of a given proteome. Proteomics adapted and applied to nutrition and health should demonstrate ingredient efficacy, deliver bio-markers for health and disease disposition, help in differentiating dietary responders from non-responders, and discover bioactive food components.