Variability in the reproducibility of protein digestion is the major source of measurement variance in stable isotope dilution, multiple reaction monitoring mass spectrometry (SID-MRM-MS), and immuno-MRM-MS (SISCAPA) assays.
This application note describes how the Agilent Bravo Automated Liquid Handling Platform was used for automated digestion in order to improve the reproducibility between experimental runs and reduce the labor intensity of this step when large numbers of samples are evaluated. A Bravo Platform at the Broad Institute was configured for automated reduction, alkylation, and proteolytic digestion of plasma from human patients and animal samples to complete this assessment. This application note compares the automated trypsin digestion of plasma in 96-well plates using the Bravo Platform to manual trypsin digestion in microcentrifuge tubes, demonstrating comparable analytical results between manual and automated methods. Automation on the Bravo Platform allows us to process up to 96 samples per day (as compared to 24 processed manually), enables parallel reagent addition, and improves lab productivity. A future report will detail our use of the Agilent Bravo in targeted immuno-MRM enrichment.