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

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.