Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers

Formalin-fixed paraffin-embedded (FFPE) tissue proteomics has emerged as a promising approach for precision medicine, offering access to vast clinical archives. Despite technological advances enabling identification of thousands of proteins from FFPE samples, no proteomic diagnostic tests based on FFPE tissues have achieved regulatory approval for clinical diagnostics, raising fundamental questions about the translational viability of this approach.

This review critically evaluates the realistic barriers preventing clinical translation of FFPE proteomics and identifies targeted applications with genuine promise for near-term implementation. We demonstrate that while comprehensive discovery-based proteomics faces insurmountable challenges including validation failure rates exceeding 90%, targeted proteomic strategies focused on specific clinical questions show substantially greater potential. Current implementation barriers extend beyond technical limitations to encompass economic constraints (5-10-fold higher costs than immunohistochemistry), regulatory uncertainties, and fundamental incompatibilities with clinical laboratory workflows. The persistent emphasis on increasingly complex analytical platforms may represent misallocated resources given unresolved standardization and validation challenges.

Strategic redirection toward targeted proteomic applications addressing specific diagnostic needs, rather than comprehensive molecular profiling, offers the most viable pathway for clinical translation. Success will require prioritizing applications where FFPE proteomics provides unique, actionable information that justifies its complexity and cost relative to established methodologies. We propose specific criteria for identifying high-impact applications and outline a pragmatic roadmap for achieving clinical implementation within realistic timeframes.