The objective of this study is to identify fish protein markers for detecting multiple species based on a comparative proteomic approach that relies on fragments with identical sequences. The possibilities and challenges of the use of peptides obtained from carp () and herring () proteins are discussed. A bioinformatic analysis was followed by an LC-MS/MS experiment to identify markers predicting the presence of fish allergenic proteins. Selected myosin peptides were found in carp protein hydrolysates with known sequences and in herring protein hydrolysates with unknown sequences. The results obtained for carp and herring proteins myosin and parvalbumin indicate that proteins with unknown sequences can be identified by peptide markers. Such markers can be designed by disregarding the principle that peptides should be unique (present in one sequence). The challenge is to determine a group of proteins that can be detected by peptide identification.