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Comparison of cartridge and bead-based sample preparation strategies for bottom-up proteome analysis of detergent-containing samples

Jessica L. Nickerson 1 , Kent MacLean2 , Alan A. Doucette 1

  1. Chemistry, Dalhousie University, Halifax, NS, Canada
  2. Proteoform Scientific, Halifax, NS, Canada

Introduction

Detergents including sodium dodecyl sulfate (SDS) are becoming increasingly accepted in proteomics workflows. This is owing to a growing list of semi-automated approaches, designed to effectively purify and digest protein mixtures ahead of bottom up LC-MS/MS analysis. Since the advent of filter-aided sample preparation (FASP) as a cartridge-based format which simplifies SDS removal and protein digestion, numerous other strategies have been reported enabling the MS acquisition of the resulting peptide digests.1 Among the cartridge and bead-based technologies are Suspension Trapping S-Trap, in-StageTip (iST), Single-Pot, Solid-Phase-Enhanced Sample Preparation (SP3), and the ProTrap XG, all of whom report successful acquisition of peptide lists from SDS-containing samples.1,2,3,4,5Here, we directly evaluate the performance of these sample preparation strategies looking at four specific figures of merit: the protein/ peptide recovery, sample purity as judged by residual level of SDS, protein digestion efficiency, and sample throughput/ process time.