Selective capillary electrophoresis

A method of separating a substance mixture sample by capillary electrophoresis comprises carrying out one or more derivatisation steps on the sample to produce a separable mixture comprising at least two groups of differently charged substances, before separating the sample by capillary electrophoresis and collecting at least on of the groups of substances. Preferably, only some of the substances undergo derivatisation to produce charged derivatives, and these may be separated from the non-derivatised substances. There may be a digestion step before or after the derivatisation. The method may be used to separate proteins in one or more proteomes. The method may be combined with a second separation step, and/or with mass spectrometry. The method may be used to determine the relative concentrations of proteins in two different proteomes, wherein the two proteomes are labelled with different isotopic markers, or to determine post-translational modification.