Functionalized magnetic nanoparticles are increasingly used as probes in biomolecule detection. We compared two different techniques, which provide information on the state of the magnetic particle system. The dynamics of an ensemble of magnetic nanoparticles was probed measuring the response its magnetisation both on an alternating magnetic field by AC-susceptometry and on a jump of external magnetic field by magnetorelaxometry. In order to compare both techniques, we studied the binding of streptavidin functionalized nanoparticles (fluidMAG/BC-SAV) to biotin-agarose beads and to biotinylated prostate specific antigens (PSA-10). By both techniques we observed specific changes in shape and amplitude of the characteristic signals due the binding of the particles. Therewith the signals of bound and unbound probes can be discriminated and a homogeneous assay without time-comsuming washing steps is realized. The AC susceptometry method provides a robust and sensitive measurement technology. Magnetorelaxometry, utilizing superconducting quantum interference devices (SQUIDs) as magnetic field sensors, owns a much shorter measurement time and has the potential of an even higher sensitivity, at the expense of a considerably increased technological effort.