Because mRNA abundance and protein amounts often are poorly related, it is important to extend the evolutionary analysis of polyploidy and domestication to the proteomic level. Using comparative proteomic approaches, including two-dimensional gel electrophoresis (2-DE) and iTRAQ, we have characterized global protein changes corresponding to polyploidization and human-mediated selection under domestication. We have identified proteins differentially expressed during cotton fiber development in wild and domesticated accessions of both G. barbadense and G. hirsutum, and have discovered how these have been altered by domestication (see Hu et al. citations on publication page). These proteins become candidates for metabolic processes underlying cotton fiber development and domestication, and for future functional analyses that may yield insight into domestication and cotton improvement. A combined proteomic and transcriptomic analysis on cotton seed development is in progress.