High-Throughput, Streamlined Processing Workflow of FFPE Tissue Yielding up to 10K Proteins/Sample

Presented by Moe Haines, Senior Research Associate II, Broad Proteomics, Broad Institute of MIT & Harvard, Cambridge, MA

Formalin-fixed paraffin-embedded (FFPE) tissue has long served as the standard for tissue preservation, representing an invaluable resource for clinical studies due to its association with patient outcomes and its link to molecular insights. Here we present a streamlined proteomic workflow aimed at overcoming current challenges associated with FFPE processing. The workflow employs the Covaris LE220-plus focused-ultrasonicator and Adaptive Focused Acoustics (AFA) technology for tissue lysis, plate-based S-Trap for proteolytic digestion, and automation for faster, more reproducible analyses. Samples are analyzed by data-independent acquisition (DIA) and are benchmarked against a TMT-based multiplexed workflow. This approach

identifies up to ~10,000 unique proteins from single-shot injections using the Orbitrap Astral MS, with a turnaround of 4 days for a full 96-well plate.