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This brief discusses incorporating an adaptive Q-parametrized compensator structure into the design of magnetic traps. This approach characterizes all stabilizing controllers using a single, stable filter, that can be used as a free parameter to tune and adapt the instrument. Q-parameterization transforms the feedback control problem into an equivalent feedforward control problem, and adaptive filter theory is used to adjust the weights of an finite impulse response to account for changing instrument dynamics and to reduce the effects of Brownian disturbances. This ensures the performance of the magnetic trap instrument meets specific performance requirements while accounting for the changing dynamics of the instrument. The adaptive system was implemented in a hardware-in-the-loop simulation. The adaptive control approach converged to a controller that exhibits disturbance rejection performance at least as good as a fixed-gain controller designed for the system.