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Updated: Jan 23, 2026

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
Published on: September 2, 2013
Proteomic insights in Acrocomia aculeata: Optimizing sample preparation techniques for analysis of an oleaginous
Wassali Valadares de Sousa1, Yara Martins da Silva2, Milene de Figueiredo3
1Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Laboratory of Proteomics (LabProt), LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
Abstract:
Proteomics of Acrocomia aculeata (macauba palm), a highly oleaginous tropical species, has been limited by its fibrous, carbohydrate- and lipid-rich tissues. This study reports the first proteomic characterization of its mesocarp and endosperm, establishing optimized workflows for mass spectrometry-based proteomics analysis. Across five tested protocols, 3223 proteins were identified in mesocarp and 942 in endosperm, including storage globulins, metabolite interconversion enzymes, translational proteins, and stress-response factors. The S-Trap (ST) method provided the best performance in the endosperm, with 239 unique proteins, enhanced recovery of Golgi and nuclear proteins, and the lowest variability (median CV ∼25%). Conversely, the phenol-saturated protocol (P-In) excelled in the mesocarp, identifying up to 2248 proteins, particularly plastidial and vacuolar classes. These findings demonstrate that protocol selection influences proteomic depth, reproducibility, and functional coverage. By delivering a robust workflow for this non-model crop, our study enables new applications in food proteomics, oil metabolism, and sustainable ingredient development.
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