Embodiments of the invention relate to a clinical instrument analyzer system for the automatic analysis of patient samples. In one embodiment, the analyzer may be used to analyze bodily fluid samples, such as blood, plasma, serum, urine or cerebrospinal fluid, for example. Embodiments of the invention relate to an apparatus and method, for example, an immunoassay method, for separating out target molecules in a magnetic field and then analyzing those target molecules with a luminometer.