From FFPE to Biomarkers: High-Throughput Proteomics for Cancer Research

Webinar Abstract Formalin-fixed paraffin-embedded (FFPE) samples are a cornerstone of clinical research, providing a stable and widely available resource for retrospective studies in biomarker discovery and disease mechanism investigation. Stored routinely in hospital pathology departments and linked to clinical metadata, FFPE specimens enable large-scale proteomic analyses. However, their use in LC-MS-based proteomics presents significant analytical challenges. Traditional methods involve labor-intensive sample preparation steps, including xylene deparaffinization and extensive protein crosslink reversal, making it difficult to scale for large clinical cohorts. This webinar introduces a novel, high-throughput workflow for FFPE proteomics, eliminating the need for xylene-based deparaffinization and enabling scalable sample preparation. By integrating BeatBox®, an automated tissue homogenizer and cell lyser, with in-StageTip (iST) technology, we demonstrate a streamlined, plate-based approach for protein extraction and digestion. This PreOmics workflow delivers high-quality, reproducible peptide and protein identifications with minimal manual intervention, making it suitable for clinical proteomics applications. We will showcase data from FFPE sections across eight different cancer types, analysed via DIA LC-MS/MS, with an initial cohort yielding 78,097 peptide identifications and 9,822 protein groups. Importantly, this approach has been validated across multiple operators and days, confirming its robustness and reproducibility. Additionally, we will explore the suitability of this workflow for multiplexing in large studies, unlocking new opportunities for high-throughput biomarker discovery. Join us to learn how this innovative workflow accelerates FFPE proteomics, enhances reproducibility, and enables large-scale clinical research with minimal sample input. Webinar Summary Formalin-fixed paraffin-embedded (FFPE) samples are essential for retrospective clinical research but present challenges for LC-MS proteomics. This webinar introduces a streamlined, scalable workflow that simplifies FFPE sample preparation, enhancing efficiency and reproducibility for large-cohort studies and unlocking new opportunities for high-throughput biomarker discovery. Our expert speakers will present data from diverse cancer samples, demonstrating robust and reproducible peptide and protein identification. They’ll outline how this approach improves high-throughput biomarker discovery by LC-MS and enables large-scale disease research using FFPE specimens. Key Learning Objectives 1. Recognize the challenges of FFPE proteomics and learn how to overcome analytical hurdles for reliable LC-MS analysis 2. Understand how a streamlined, high-throughput workflow improves reproducibility in clinical research 3. Learn how enhanced FFPE proteomics workflows accelerate biomarker discovery in large-cohort cancer studies 4. Explore the role of BeatBox® and iST technology in simplifying FFPE sample processing Silvia Wuertenberger, PhD Senior Product Manager Silvia joined PreOmics in 2022 as Product Manager and is responsible for BeatBox® and Proteomic Sample Preparation products. She holds a PhD in Biology from Eberhard-Karls-University Tuebingen, and is an expert in protein biochemistry and analytical technologies to measure protein attributes. Prior to PreOmics, Silvia gained experience in commercialization and development of analytical instruments for drug discovery and development at NanoTemper Technologies. Jessica Moore, PhD Senior Scientist Discovery Life Sciences Dr. Jessica Moore is passionate about proteomics and its potential to improve human health. She is currently a Huntsville Alabama-based Senior Scientist at Discovery Life Sciences, where she focuses on sample preparation approaches and non-invasive biomarker discovery. She is dedicated to helping collaborators use novel technologies and multiomics to study biological systems, furthering our understanding of disease progression, prognostics, and mechanisms of action. Her background is in analytical chemistry. She graduated from Murray State University in 2009 with a B.S. in Chemistry and Music and earn an M.S in Analytical Chemistry before completing her doctorate at Vanderbilt University in 2016. With 14 years of experience in mass spectrometry, she has worked in diverse teams of scientists, pathologists, clinicians, and researchers.