The majority of protein-interaction sites are discontinuous, this means that various loops form the three-dimensional binding pocket. For proteins with unknown sequence and structure random libraries can be used to define the interaction site [1]. Proteins with a defined sequence and/or structure can be scanned with overlapping peptides against, for instance, monoclonal antibodies. However, testing monoclonal antibodies in ELISA against all overlapping 12- to 15-mer peptides from these proteins is not always successful. Scanning against 25- to 30-mer peptides [2] reveals more information, since these peptides cover a larger area of the protein surface. However, to discover complete discontinuous interaction sites that contain different parts of the epitope — which are (far) apart in the primary sequence, but are brought close spatially in the protein — we developed the matrix scan. The method consists of making all possible peptides that comprise two or more different regions from a protein. The scan includes also branched combinations. Screening of these peptides provides clear insight into the nature and composition of the discontinuous epitopes as demonstrated for FSH (Follicle Stimulating Hormone).