In this webinar, a comparison of two mass spectrometry-based approaches for multiplex detection of residual allergens in food matrices will be discussed. As it will be presented, the Thermo Scientific™ Exactive™ Orbitrap mass spectrometer enabled untargeted, data independent acquisition at the highest resolving power, generating extracted ion chromatograms based on the accurate masses of the selected marker ions along with their respective fragments. As an alternative, the use of the Thermo Scientific™ LTQ Velos™ linear ion trap mass spectrometer allowed high speed data dependent MS/MS acquisition to search for proper peptide markers and transitions to be further implemented in an SRM method.