Paramagnetic beads have considerable potential as identification tags in biological analysis. For example, magnetic sensor- based arrays using the magnetic field generated by paramagnetic beads to test hybridization between interacting molecules have attracted widespread interest in recent years. However, application of paramagnetic beads as identification tags is still limited, since they do not permit differentiation between samples for multiplex analysis. Here, we report the application of a novel encoding of paramagnetic beads with peptide sequences. This strategy allows DNA samples labeled with peptide- encoded paramagnetic beads to be identified by the selective enzymatic cleavage of each peptide cross- linker.