Proteomic analysis of non-model plants requires selecting appropriate sample preparation techniques to reliable and comprehensive results. Acrocomia aculeata, a high-yielding, adaptable palm native to Tropical America, poses proteomic analysis challenges due to its undomesticated status and genetic variability. To cope withthis issue, we applied different sample preparation protocols for the proteomics analysis of A. aculeata endosperm and mesocarp tissues.