A method and apparatus for performing separation of molecules, in particular biomolecules such as nucleic acids and peptides, are disclosed. The method comprises separating molecules by a first characteristic along a linear dimension of a channel, and separating the molecules by a second characteristic along the same linear dimension, with the rust and second separations being carried out within at least partially overlapping sections of the channel. The two separations may then be combined to give a virtual two-dimensional separation which is carried out in a single dimensional real space. The method may also include detecting molecules during the second separation, preferably using an intrinsic characteristic of the molecules for example UV absorbance.

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