Detecting contaminations of unexpected species in food is essential for the health of the growing population who are allergenic to traces of milk or egg. The detection of these traces is difficult with the current analytical methods, which are mainly based on DNA or antibody-based techniques. DNA/RNA based techniques are highly sensitive, but in modern food the DNA is often degraded due to the processing methods used during the manufacturing processes. Antibodies can vary from batch to batch and are dependent on the presence of the recognized antigen, which can be heat-labile. The use of mass spectrometry-based proteomics promises to solve this problem, as proteins are more stable and the primary amino acid sequence cannot be changed during a baking process. Here we propose to develop a method for the detection of egg and mild in baked goods, based on robust targeted proteomics.