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March 21, 2026Journal of Proteome Research0 citations

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

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YLYingjie LiLZLi ZhouLXLi Xia

Key Points

  • The study aims to evaluate how long-term storage affects proteomic analysis of colorectal adenocarcinoma FFPE samples.
  • Analyzed 80 colorectal adenocarcinoma FFPE samples, comparing >15 years and <1 year storage.
  • Employed standardized protein extraction and mass spectrometry workflows for profiling.
  • Evaluated protein extraction efficiency, peptide yields, and post-translational modification identification.
  • Conducted biological enrichment analysis using Gene Ontology and KEGG.
  • Storage time impacted protein extraction efficiency and peptide yields more significantly.
  • Biological enrichments were consistent regardless of archival time.
  • Five clinically relevant biomarkers were validated through immunohistochemistry.
  • FFPE tissues remained stable for proteomic analysis even after >15 years.

Abstract

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.

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Cite This Study

Li et al. (2026) studied this question.

synapsesocial.com/papers/69be36086e48c4981c674abbhttps://doi.org/10.1021/acs.jproteome.5c01070
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