Proteomic insights in Acrocomia aculeata: Optimizing sample preparation techniques for analysis of an oleaginous alternative crop

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.