Automated Electrokinetic Platform for High-Throughput Sodium Dodecyl Sulfate Depletion Ahead of Proteome Analysis by Mass Spectrometry

Sodium
dodecyl sulfate (SDS) provides numerous benefits for proteome
sample preparation. However, the surfactant can be detrimental to
downstream mass spectrometry analysis. Although strategies are available
to deplete SDS from proteins, each is plagued by unique deficiencies
that challenge their utility for high-throughput proteomics. An optimal
approach would rapidly and reproducibly achieve less than 10 ppm residual
SDS while simultaneously maximizing analyte recovery. Here, we describe
improvements to a simple electrokinetic device termed transmembrane
electrophoresis, which we previously reported for automated, rapid
SDS depletion of proteome samples. Voltage-driven transport of SDS
across a molecular weight cutoff membrane is enhanced at higher electric
fields, which is herein achieved by integrating an active cooling
mechanism to mitigate the impacts of Joule heating. We report 99.9%
reduction of SDS (final concentration < 5 ppm) in 5 min. The device
is employed in a detergent-based proteomic workflow for analysis of
an enriched yeast membrane proteome extract, demonstrating quantitative
protein recovery (>98%) and increasing the number of identifications
by liquid chromatography-tandem mass spectrometry.