Introduction and Objectives
Two decades of proteomics research have culminated in development of high resolution, high speed, and high sensitivity LC-MS instruments. Sample preparation methods have experienced less attention and often rely on traditional approaches developed for proteomes of biological fluids. However, a recent paradigm shift to precision medicine requires emphasizing tissue proteomics as one of the cornerstones of understanding cancer and development of personalized approaches to treatment. Modern proteomics techniques, such as DIA and SWATH-MS, require high quality sample preparation methods that minimize sample losses to maximize proteome coverage. High–throughput proteomic analysis of tissue biopsies presents particular challenges with respect to complete protein extraction, solubilization and digestion. Traditional methods of tissue sample preparation typically involve manual sample handling and multi-step procedures that inevitably lead to loss of analytes due to sample transfer steps. The goal of the current study was to further optimize this protocol in order to minimize manual sample handling and sample preparation time, while maximizing quantitative recovery of proteotypic peptides.