A system for separating an analyte of interest from other components of a sample contained in a receptacle (160, 162), said system comprising: a receptacle holding station configured to receive and hold a receptacle (160, 162) delivered to said receptacle holding station by a receptacle transport, said receptacle holding station including one or more stationary magnets positioned to apply a magnetic field to the contents of said receptacle (160, 162) held in said receptacle holding station and a top panel over said receptacle (160, 162) held in the receptacle holding station; a magnetic separation station comprising one or more magnets (220, 222), said magnetic separation station being constructed and arranged to perform a magnetic separation procedure on the contents of said receptacle (160, 162) transported from said receptacle holding station to said magnetic separation station by a receptacle transport by magnetically isolating an analyte immobilized on a magnetically-responsive solid support and removing other components of the sample from said receptacle (160, 162); and a receptacle transport configured to automatically move said receptacle (160, 162) between the receptacle holding station and the magnetic separation station, wherein the receptacle transport is controlled to transfer said receptacle (160, 162) from the receptacle holding station to the magnetic separation station after said receptacle (160, 162) has been held in the receptacle holding station for a specified dwell time, and wherein the magnetic separation station is controlled to perform the magnetic separation procedure by performing at least a first step of removing fluid contents from said receptacle (160, 162) transferred to the magnetic separation station after the contents of the receptacle (160, 162) have been subjected to a magnetic field from the one or more magnets (220, 222) of the magnetic separation station for at least an initial dwell time within the magnetic separation station, wherein the initial dwell time within the magnetic separation station is less than the specified dwell time within the receptacle holding station. a receptacle holding station configured to receive and hold a receptacle (160, 162) delivered to said receptacle holding station by a receptacle transport, said receptacle holding station including one or more stationary magnets positioned to apply a magnetic field to the contents of said receptacle (160, 162) held in said receptacle holding station and a top panel over said receptacle (160, 162) held in the receptacle holding station; a magnetic separation station comprising one or more magnets (220, 222), said magnetic separation station being constructed and arranged to perform a magnetic separation procedure on the contents of said receptacle (160, 162) transported from said receptacle holding station to said magnetic separation station by a receptacle transport by magnetically isolating an analyte immobilized on a magnetically-responsive solid support and removing other components of the sample from said receptacle (160, 162); and a receptacle transport configured to automatically move said receptacle (160, 162) between the receptacle holding station and the magnetic separation station, wherein the receptacle transport is controlled to transfer said receptacle (160, 162) from the receptacle holding station to the magnetic separation station after said receptacle (160, 162) has been held in the receptacle holding station for a specified dwell time, and wherein the magnetic separation station is controlled to perform the magnetic separation procedure by performing at least a first step of removing fluid contents from said receptacle (160, 162) transferred to the magnetic separation station after the contents of the receptacle (160, 162) have been subjected to a magnetic field from the one or more magnets (220, 222) of the magnetic separation station for at least an initial dwell time within the magnetic separation station, wherein the initial dwell time within the magnetic separation station is less than the specified dwell time within the receptacle holding station.