In this review, we outline the state-of-the-art of proteomic techniques and their application within the plant-based food industry. The relevance of high throughput proteomic approaches is to increase insight and understanding of how food processing is affected by the physiology of the product and through this, to enable the optimization of the overall food production process. Food areas with large potential for application of proteomics technologies are discussed, including novel and controversial areas such as food irradiation, GMOs, non-thermal processing, obesity, and functional foods.