Method optimization for FFPE proteomics of hepatocellular carcinoma

ABSTRACT: Archival formalin-fixed, paraffin-embedded (FFPE) tissues are invaluable resources for translational research, as clinical outcomes and treatment histories are often available. FFPE blocks provide a standardized and cost-effective alternative to frozen specimens, with formalin-induced protein crosslinking enabling stability for decades at room temperature. However, these crosslinks hinder efficient protein extraction, limiting the application of mass spectrometry–based proteomics to archival samples. We systematically compared three protein extraction workflows—adaptive focused acoustics (AFA) with Covaris buffer, AFA with SDS buffer, and SP3 with SDS buffer—using hepatocellular carcinoma (HCC) tissues.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Sumio Ohtsuki 

PROVIDER: PXD070191 | JPOST Repository | Tue Oct 06 00:00:00 BST 2026

REPOSITORIES: jPOST