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Automating Protein Digestion for Reproducible Proteomics

There are many steps in the process to generating high quality proteomics data on biological samples. There are now powerful MS workflows for quantitation (MRM and SWATH® acquisition) that enable highly reproducible quantitation on small or large numbers of samples. This creates a new bottleneck in sample preparation, the ability to reproducibly generate digested proteomic samples is critical for performing protein quantitation studies.

By using automation, the day-to-day variability of multi-step protocols such as protein denaturation, reduction, alkylation and digestion can be significantly reduced. Removing the labor intensiveness of MS sample preparation frees up scientists to do higher value work on other aspects of projects. Here, we adapted a reliable protein digestion protocol for use on the Biomek NXP Span-8 Workstation1. This was coupled with an optimized protein preparation kit2 that provides ready to use reagents for reproducibility and efficiency.