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Two rice cultivars, IAC1131 (drought tolerant) and Nipponbare (drought sensitive), with contrasting genetic backgrounds and levels of tolerance to drought, were analysed using both label-free and tandem mass tags (TMTs) quantitative proteomics approaches, aiming to elucidate the mechanisms of drought tolerance. Four-week-old seedlings of both cultivars were grown in large soil volumes in the glasshouse under controlled conditions and then exposed to moderate and extreme drought for 7 days, followed by 3 days of re-watering period. Mature leaves were harvested from plants of each treatment for protein extraction and subsequent complementary shotgun proteomic analyses. The data from this study are related to the research article “Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease” (Wu et al., 2016) [1].