Systematic Evaluation of the Impact of Storage Time on Label-Free Proteomics of Colorectal Adenocarcinoma Formalin-Fixed Paraffin-Embedded Tissues

Mass spectrometry (MS)-based proteomics has empowered comprehensive protein profiling of biological specimens. However, formalin-fixed paraffin-embedded (FFPE) tissuescritical resources for clinical biomarker discovery-remain underexplored in the setting of long-term storage (>15 years). Herein, we systematically evaluated the impact of storage time on proteomic analyses of 80 colorectal adenocarcinoma (CRC) FFPE samples, which were stratified by two key variables: storage time (>15 years vs 15 years of storage, thereby providing critical insights for leveraging archival FFPE biobanks to advance clinical proteomics and archival pathology research.