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Rapid and automated SDS depletion from intact proteins for top down proteome analysis

Alan A. Doucette; Nicole Unterlander; Subin Rajendran; Philip Jakubec; Khaldun Al Azzam
Department of Chemistry, Dalhousie University

Introduction

SDS is favored for protein solubilization and mass fractionation (GELFrEE), but severely compromises top down proteome (TDP) analysis. 100 ppm (0.01% SDS) defines the upper tolerance5, though <10 ppm is required to fully avoid SDS suppression. Acetone precipitation achieves this level of purity6; with aid of a disposable cartridge (ProTrap XG), aggregated proteins are retained in high yield.1 Alternatively, a fully automated device termed TME, or transmembrane electrophoresis, purifies intact proteins in solution, with aid of an applied electric field.2-4 Though high recovery and purity was obtained, our initial TME runs required ~1 hour, being limited by Joule heating. Here we augment SDS depletion by TME to <10 min, permitting TDP.