Proteomic comparison of human brain tissue preservation methods
Laura Plantera1, Anna Didio2, Uta Ceglarek2
1Institute of Anatomy, Leipzig University, Liebigstraße 13, 04103 Leipzig, Germany.
Journal of Proteomics
|January 1, 2026
Summary
Formalin-fixed brain tissue closely mirrors fresh-frozen proteomic profiles, offering a reliable resource for neurodegenerative disease research. This study validates formalin fixation for valuable proteomic analysis.
Area of Science:
- Neuroscience
- Biochemistry
- Proteomics
Background:
- Proteomics is crucial for understanding the human brain.
- Tissue preservation methods, such as formalin-fixation and paraffin-embedding (FFPE), are common but can impact proteomic analysis.
- Comparing different preservation methods is essential for maximizing the utility of valuable human brain tissue samples.
Purpose of the Study:
- To investigate the impact of different tissue preservation methods (formalin-fixed, FFPE, fresh-frozen) on protein profiles.
- To evaluate the suitability of formalin-fixed tissue for proteomic analysis, particularly for neurodegenerative disease research.
- To identify potential protein biomarkers in formalin-fixed samples from Alzheimer's disease patients.
Main Methods:
- Proteomic analysis using reversed-phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS) with data-independent acquisition (DIA).
- Comparison of protein profiles from fresh-frozen, formalin-fixed, and FFPE human brain tissues.
- Analysis of a pilot cohort with varying stages of Alzheimer's disease (AD).
Main Results:
- Formalin-fixed samples showed proteomic profiles more similar to fresh-frozen tissues than FFPE samples.
- A core set of 1753 proteins was consistently detected across all preservation methods.
- Quantitative analysis revealed underrepresentation of certain cellular processes in fixed tissues, while neuronal development pathways were overrepresented.
- 12 potential protein biomarkers, including nucleosomal proteins and carboxypeptidase M (CPM), were identified in formalin-fixed samples from AD patients.
Conclusions:
- Formalin-fixed brain tissue is a valuable and reliable resource for proteomic studies, especially in neurodegenerative disease research.
- The study validates a protein extraction protocol for formalin-fixed samples, enabling future biomarker discovery.
- Formalin fixation offers a good balance between tissue preservation and proteomic data integrity.
