A method for removing an ionic liquid from an aqueous sample is provided. In some embodiments, the method includes: (a) combining an aqueous sample including an ionic liquid with an ion exchanger composition including an ion exchanger counterion to produce a solution including a fluorous salt of the ionic liquid, where at least one of the ionic liquid and the ion exchanger counterion is fluorinated; (b) contacting the solution with a fluorous affinity material, thereby removing fluorous salt from the solution and producing an aqueous eluate; and (c) collecting the aqueous eluate. In certain embodiments, the method further includes: contacting a cell with an ionic liquid composition to lyse the cell and produce an aqueous sample; and contacting the aqueous sample with a reverse phase substrate, thereby adsorbing proteins and/or lipids of the cell on the substrate. Compositions, kits and systems for practicing the subject methods are also provided.