A simple protein extraction method for proteomic analysis of mahogany (Swietenia macrophylla) embryos

In any proteomic studies, protein extraction and sample preparation are the most crucial steps for obtaining optimal results. This is to ensure extracted proteins are not only high in yield but also clean from contaminants that could affect downstream proteomic applications such as two dimensional gel electrophoresis (2-DE) and mass spectrometry. Tissues from plants and trees such as Swietenia macrophylla are often rich in non-protein contaminating substances, which could interfere in the proteomic applications. S. macrophylla or also known as the mahogany is one of the most valuable tree species in the world. Studies on proteins for this tree as well as its seeds are very limited. We have extracted proteins from S. macrophylla seeds (specifically embryo tissues) using three different methods, each having different lysis buffer recipes. Furthermore, another set of samples were precipitated using trichloroacetic acid/acetone prior to the three extraction methods to further purify the protein samples. The results from 2-DE analysis showed approximately 240 protein spots were detected from the successful protocol using a lysis buffer of 9 M urea, 4% CHAPS, 0.5% triton X-100 and 100 mM DTT without TCA/acetone precipitation. This study highlights the aspects of sample preparation for S. macrophylla embryos, focusing on the total protein extraction and resolution in SDS-PAGE as well as 2-DE. Furthermore, this is the very first report of the proteome 2DE profile from S. macrophylla embryo.