The disclosed methods use a multi-phase system to separate samples according to the density of an analyte of interest. The method uses a multi-phase system that comprises two or more phase-separated solutions and a phase component such as a surfactant or polymer. The density of the analyte of interest differs from the densities of the rest of the sample. The density of the analyte of interest is substantially the same as one or more phases. Thus, when the sample is introduced to the multi-phase system, the analyte of interest migrates to the phase having the same density as the analyte of interest, passing through one or more phases sequentially.