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Cotton today is one of the most important economic crops. Cotton fiber is the most used material for the textile industry, and takes an important strategic status in the world economy. Proteomics is one of the most important techniques in the post-genome era, and two-dimensional electrophoresis (2-DE) is one key technology for proteomics. Protein extraction and sample preparation are of prime importance for optimal 2-DE results (Isaacson et al., 2006). The cotton is a highly recalcitrant plant material and rich in compounds such as polysaccharides, polyphenols, nucleic acids, cellulose, and other secondary metabolites, which interfere with protein extraction, produce highly diluted protein extracts, and affect protein migration in 2-DE (Gorg et al., 2000). Moreover, modified or different protein extraction method should be used for different cotton tissues (e.g., leaves, roots, seeds, and stems), which contain different secondary metabolites. Here, several protocols to extract total proteins for different cotton tissues are described based on methods routinely used in our laboratory.

Preparation of Protein Samples for 2-DE from Different Cotton Tissues