Abstract
Gel-based comparative proteomics approach is a valuable technique for studying the changes in abundance of proteins in any given system. The combination of this technique with mass spectrometry has provided immense insight into protein dynamics during fruit development and ripening. This chapter describes, informatively, the procedures for carrying out comparative proteomics analysis of date palm (Phoenix dactylifera L.) fruits at different developmental stages using a combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometry. A comparative proteomics approach provides an overview of protein abundances during fruit maturation and insights into proteins that play key roles during fruit maturation. Moreover, 2-DE technique enables the visualization of total protein distribution and abundance in addition to providing a comparative platform following separation of complex proteins based on their molecular weight and isoelectric point. Overall, this chapter describes methodologies for extraction of proteins from a high carbohydrate-containing fruit, protein quality assessment using one-dimensional gel electrophoresis (1-DE), separation using 2-DE, comparative analysis using Delta2D v4.6, processing of spots of interest, and protein identification using mass spectrometry. This protocol is important for studies aiming at comparative proteomics to gain insights into changes of protein abundances in tissues and organs in general and date palm fruits, in particular.