iTRAQ labeling combined with LC-MS/MS analysis quantitative proteomics techniques were employed to compare proteome of cotton seedling cultured with floating nursery or nutrient pot method in this paper. Total 169 differentially expressed proteins were identified including 116 up-regulated and 53 down-regulated proteins. GO, COG and KEGG-pathway analysis of these identified proteins reveals that 12% of them were involved in water stress response of cotton. Moreover, the research draw a previous conclusion that aerobic respiration of cotton root bred with floating nursery method is suppressed w...