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Streamlining Bottom-up Sample Preparation: Assessing digestion efficiency in cartridge and bead-based technologies

Jessica L. Nickerson , Alan A. Doucette, Dalhousie University, Halifax, Canada


A variety of commercially available bottom-up sample preparation technologies—namely FASP, S Trap, iST, SP3 and the ProTrap XG—employ unique digestion strategies to optimize the subsequent LC-MS/MS analysis of a proteome. The respective approaches involve elevated temperature, dual enzyme systems, concentrated enzyme, and overnight incubation with the objective of improved digestion efficiency.

It is of interest to herein assess the available technologies on the basis of digestion efficiency and to determine whether these efficiencies can be reproduced in-solution.