Comparison of protein extraction methods for 2DE-based proteomic analysis of duckweed Spirodela polyrhiza, a small aquatic model plant

Abstract Duckweed, a small floating aquatic plant in the family Lemnaceae, has considerable potential for agricultural and environmental applications. Proteomic analysis will facilitate the study of plant biology and plant-environment interactions. A reliable and reproducible protein extraction method is critical for successful proteomic analysis. To date, there have been no evaluation studies of extraction methods for duckweed proteomics. In this study, we developed a trichloroacetic acid (TCA)/acetone/TCA precipitation method (TAT) for Spirodela polyrhiza and compared it with three extraction methods, primarily by two-dimensional gel electrophoresis (2DE). These methods were based on TCA/acetone precipitation, phenol extraction or their combination to concentrate proteins and remove interfering substances. As a result, these methods produced significant differences in protein yield, and each revealed a unique set of proteins. In general, TAT produced better 2DE protein patterns with high reproducibility regarding the number, coverage and abundance of protein spots. Our results provide useful information for selecting suitable extraction methods for proteomic analysis of duckweed plants.