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The availability of analytical methods to detect and determine levels of markers of priority allergens in foods is of the utmost importance to support standard setting initiatives, the development of compliance and enforcement activities, as well as to provide guidance to industry on implementation of quality control practices, ensuring the effectiveness of allergen-related sanitation techniques. This paper describes the development and implementation of a mass-spectrometry-based technique to determine markers for individual sources of gluten in beer products. This methodology was shown to answer the requirements of Health Canada's proposed labeling standard for individual gluten source declaration, in order to achieve its policy objectives (i.e., protection of sensitive consumers, while promoting choice). Minimal sample work-up was required and the results obtained by ELISA were further complemented using the LC-MS/MS method. This paper aims to demonstrate the feasibility of alternative techniques to ELISA-based methodologies to determine allergen and gluten markers in food.