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The application of quantitative proteomics to food analysis is in its infancy. This is partly due to the diverse range of plant and animal species consumed as foods, many of which are not sequenced, making annotation of food proteomes difficult. In addition food processing procedures and interactions with other food components, such as lipids and starch, introduce a diverse range of chemical and conformational changes to proteins, many of which are poorly defined. Mass spectrometry-based molecular profiling has great potential as quality assurance tool for food authenticity and traceability, safety and quality. A driver for the application of quantitative protein mass spectrometry-based methods to food has been the need to develop confirmatory methods for allergen analysis in support of food allergen labelling regulations. In addition to providing rigorous quantitative methodology for complex biomacromolecules, protein mass spectrometry is also allowing us, for the first time, to discover how processing procedures modify the foods we eat at a molecular level. Such knowledge is essential if we are to understand how food processing can be used to optimise the beneficial health effects of foods.

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