In the present study, we found that Nipponbare and IAC1131 behave equivalently in response to multiple abiotic stress, which included simultaneous application of drought, salt and temperature stress. At the level of molecular analysis by isotopic labelling quantitative proteomics, 6215 proteins were reproducibly identified and quantified across the two genotypes and three time points sampled. Heat shock proteins, late embryogenesis abundant proteins, and photosynthesis-related proteins were all found to be differentially abundant in response to stress treatments in both Nipponbare and IAC1131.