Standardized and automated solid-phase extraction procedures for high-throughput proteomics of body fluids

In order to balance the speed of analytical sample preparation procedures with mass spectrometry (MS)-based clinical proteomics the application of high-throughput robotic systems for body fluid workup is essential. In this paper we describe the implementation of various solid-phase extraction (SPE) sample preparation protocols on two different platforms, namely: 1) Magnetic bead-based SPE of peptides and proteins from body fluids on a Hamilton liquid handling workstation; 2) Cartridge-based SPE on a SPARK Symbiosis system. All SPE protocols were optimized for MS-based proteomics and compared with respect to obtained peptide- and protein profiles. Throughput numbers that were achieved in a 24 hour time frame for the sample workup procedures were more than 700 samples for the magnetic bead-based method and over 1000 samples for the cartridge-based method.

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► Fully automated strategies for body fluid sample preparation are presented.
► Cartridge- and magnetic bead based SPE methods are evaluated and compared.
► Daily throughput is up to 700 samples for the magnetic bead-based method.
► Daily throughput is up to 1000 samples for the cartridge-based method.