Speaker
Description
Achieving deep proteoform coverage in top-down proteomics critically depends on effective sample pre-fractionation. To address this, we developed PEPPI-MS (Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS) in 2020, leveraging the widely used SDS-PAGE method in biochemistry as a tool for pre-fractionation. PEPPI enables efficient passive extraction of intact proteins from gels, offering a simple, cost-effective, and highly reproducible workflow. Since its introduction, PEPPI has been adopted in various top-down proteomics studies, and more recently, its importance is becoming increasingly more recognized in middle-down proteomics as well. Its potential applications include disease biomarker discovery in top-down/middle-down proteomics although high-throughput processing of large sample cohorts remains a major challenge at present. Automation of the workflow will therefore become essential. In this presentation, we introduce "PEPPI-SP3," our latest workflow combining PEPPI with the magnetic bead-based SP3 method, an established platform for automated sample preparation in bottom-up proteomics, as a promising step forward toward future automation in proteoform-level proteomics.
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