Worldwide, food-allergy-related diseases are a significant health problem. While the food industry works on managing cross-contaminations and while clinicians deal with treatment, laboratories must develop efficient analytical methods to ensure detection of hidden allergens that can cause severe adverse reactions. Over the past few years, huge progress has been made in mass spectrometry for the analysis of allergens in incurred and processed foodstuffs, especially as regards sample preparation and enrichment (solid phase extraction, protein precipitation and ultrafiltration). These achievements make it possible to meet the Allergen Bureau's Voluntary Incidental Trace Allergen Labelling (VITAL) sensitivity criteria. The present chapter details the different steps in the development of mass spectrometry methods, from peptide selection to the validation of qualitative and quantitative methods. The chapter focuses mainly on studies performed with incurred and processed food samples to ensure the applicability of the methods to allergen detection in real food products.