Abstract: Capillary electrophoresis methods for determining the relative amount of protein in a sample comprising a population of proteins are provided. The methods comprise charge and/or size separation of a target protein or a plurality of target proteins present in a sample, for example a biological sample, by capillary electrophoresis in a separation matrix comprising a haloalkane compound, and downstream detection and quantification of the total amount of protein in the sample. Optionally, the method further comprises detection and quantification of one or more specific target proteins in the sample. Systems for carrying out the methods are also provided.