Assessment, Development, and Improvement of SDS Depletion Strategies in Mass Spectrometry Proteomic Workflows

Abstract

In proteomics, sodium dodecyl sulfate negatively affects trypsin digestion, chromatography, and mass spectrometry, thus, its effective depletion is critical to any protein sample workflow. A quantitative assessment of SDS depletion protocols reveals that acetone precipitation outperforms other methods in terms of SDS depletion, protein recovery, and number of protein identifications. Despite this, the need for precise pipetting challenges the reproducible success of precipitation and has prevented its wide spread use. Transmembrane electrophoresis (TME) is thus presented as a facile approach to protein purification. TME uses an electric potential to drive SDS through a dialysis membrane, while trapping protein in the sample chamber. It is amenable to both bottom-up and top-down approaches and is compatible with membrane proteins. Constant current enabled SDS depletion in 1 hour, though temperature control at constant power provides a faster rate of SDS depletion (10 min) without compromising recovery, making the device valuable to proteomic workflows.