The supernatant consists of non-particular cells and particles which can be discarded, leaving only your pure focus on cells connected towards the bead. Fig. 1: Workflow of a standard protein purification procedure applying magnetic beads/MagBeads. In-depth requirements of the individual techniques regarding how to use magnetic beads are supplied in https://lingjunbio.quora.com/Introduction-to-Magnetic-Beads-Biomagnetic-beads-are-high-tech-microspheres-that-integrate-magnetic-and-biological-func