Disclosed is a mixed mode chromatography method for separating correctly folded from incorrectly folded conformations of a given protein. The method is highly effective in separating correctly folded etanercept from incorrectly folded etanercept and aggregates in commercially attractive yields capable of affording etanercept preparations having very high purity in terms of correctly folded etanercept versus incorrectly folded etanercept. The invention is further directed to protein preparations and formulations comprising correctly folded proteins obtained using the present methods, and methods of treatment using the high purity preparations obtained from the mixed mode method.本發明揭示分離特定蛋白質之正確摺疊構型與不正確摺疊構型的混合模式層析方法。該方法高度有效地分離正確摺疊之恩博(etanercept)與不正確摺疊之恩博及聚集物,以具有商業吸引力之產量能夠提供具有極高純度之正確摺疊之恩博對不正確摺疊之恩博之恩博製劑。本發明進一步係關於包括使用本發明方法所獲得正確摺疊蛋白質之蛋白質製劑及調配物,以及使用自該混合模式方法獲得之高純度製劑治療的方法。