Advances in Automated Protein Sample Preparation for Biopharma and Proteomics

SECTION 1: A Universal and High-Throughput Proteomics Sample Preparation Platform -
Proteomics has become an essential tool to address critical biological questions through the identification and characterization of total protein content within a biological system. A proteomics-based high-throughput compound screening approach that applies mass spectrometry analysis is a promising approach as it can provide more comprehensive information compared to other methods, which improves the probability of success for drug development efforts. To make it feasible, we report the development of a highly automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. We systematically optimized the liquid transfer parameters during the digestion process using a Bravo liquid handling system. Digestion efficiency was excellent in comparison to a commercial digest peptide standard with minimal sample loss while improving sample preparation throughput by 20- to 40-fold (the entire process from plated cells to clean peptides is complete in ~300 min). Selected protein was further quantified using a developed HPLC-MRM method for HeLa digests with heavy labelled internal standard peptide spiked in. Excellent linearity was achieved across different cell numbers indicating a potential for target protein quantitation in clinical research.

SECTION 2: Improve Data Quality, Reduce Time to Results, and Simplify Documentation with New Sample Prep Applications and AssayMAP Software Enhancements:
Ensure the highest possible data quality for your protein analysis workflows by ensuring that the samples going into your analytical instrument are of the utmost quality possible. The AssayMAP Bravo platform is the right instrument to achieve this goal and now it is even more powerful with the addition of applications for rapid protein digestion (SP3) and high-resolution separation (automated Evosep tip loading) upfront of mass spec analysis. The best technology is only as good as the software controlling it which in the case of the AssayMAP Bravo, is easy to use, simplifies documentation with automated report generation, and has the flexibility to work in both discovery and highly regulated labs which is empowered by the optional 21 CFR Part 11 enabling features.