Electro-ultrafiltration to remove sodium dodecyl sulfate in proteins extracted for proteomics

Sodium dodecyl sulfate (SDS) is commonly used to extract membrane proteins in proteomics studies; however, it can reduce the efficiency of tryptic digestion and interfere with the results of liquid chromatography-mass spectrometry (LC-MS) analysis. Available methods for removing surfactants, such as ultrafiltration, acetone precipitation, and gel electrophoresis, are not completely satisfactory. Therefore, in this study, a new method for the depletion of SDS was established, named electroultrafiltration, and its performance was compared with other conventional pretreatment methods. Electro-ultrafiltration combines electrophoresis and ultrafiltration to remove SDS from protein samples. This method uses an electric field as the driving force and an ultrafiltration membrane as the separation medium. The performance of the electro-ultrafiltration method in terms of both the signals of LC-MS and the number of proteins identified was superior to that of simple ultrafiltration, but was slightly worse than that of acetone precipitation. These results demonstrate that the electro-ultrafiltration method could help to reduce the influence of SDS on protein digestion and identification, demonstrating its feasibility for application in proteomics.