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The screening of crude natural product extracts can be problematic, especially in enzyme/protein-based assays, due to promiscuous inhibitors and interference compounds, while high salt and lipid content can significantly dilute compounds of interest. Described herein is a simple method for high-throughput fractionation of crude extracts that can help address some of these issues. Results obtained indicate a significant improvement in assay hit rates without a reduction of hit quality and show how prefractionation aids the discovery of compounds that would be undetected by screening crude extracts alone.