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Membrane-based SDS depletion ahead of peptide and protein analysis by mass spectrometry

Nicole Unterlander, Alan A. Doucette
Department of Chemistry, Dalhousie University

Introduction

SDS interferes with both bottom-up and top-down MS analysis and must be removed prior to detection1. For bottom-up proteomics (BUP), a popular depletion method is FASP, however sample losses can often be 50% or greater2,3. Acetone precipitation is favoured for top-down proteomics (TDP), which we have shown can be done inside a centrifugal membrane filter cartridge to enhance reproducibility4. Our group recently introduced an electrophoretic purification method called transmembrane electrophoresis (TME) as an alternative depletion strategy for both BUP and TDP studies (Figure 1)5. Here we benchmark the effectiveness of TME as compared to these two popular SDS-depletion methods