A control device for a sample separation apparatus, the sample separation apparatus including a first separation unit and a second separation unit downstream of the first separation unit and supplied with the fluidic sample after treatment by the first separation unit. A control device is configured for controlling the first separation unit to execute a primary separation sequence within a time interval for separating the fluidic sample into fractions, and for controlling the second separation unit to execute secondary separation sequences within the time interval for further separating the separated fractions into sub-fractions, wherein the secondary separation sequences form part of a common sample separation method defined by a common specification of the sample separation involving a set of parameters, and adjusting, over a progress of the primary separation sequence, at least one parameter according to which at least one of the plurality of secondary separation sequences is executed.