Fusion of two proteins has become an important tool in biotechnology. Whereas biotechnological methods easily can produce C-terminal to N-terminal fused compounds, methods to couple two proteins to each of their C-termini are not easily accessible. Herein, peptides are used as models for larger proteins. A method is described exploiting the possibility to attach different reactive handles to their C-termini using a reaction catalyzed by the enzyme carboxypeptidase Y (CPY). It is possible to attach pairs of reaction handles which can react with each other to each of the peptides to be coupled. In a second step, the two modified peptides can be linked together by a chemical reaction, such as an oxime-forming reaction or a copper(I) catalyzed [2+3]-cycloaddition reaction of an azide with an alkyne.