Proteomic studies in plants including rice (Oryza sativa) and grapes (Vitis vinifera) have become increasingly prevalent in recent years now that complete genome sequences are available for both species. In our laboratory we have carried out a number of different studies involving analysis of differential protein expression in both plants and cell cultures, induced by exposure to different abiotic stress conditions. This has included detailed analysis of the response of grape cells to a wide range of temperature stresses, identification of proteins affected by changes in day length in riverbank grapes, and detailed quantitative analysis of temperature and drought stress in rice. This work was all performed using shotgun proteomics analysis with nanoLC-MS/MS, coupled with calculation and measurement of normalised spectral abundance factors using software developed in-house. This analytical pipeline enables the identification and quantitation of thousands of proteins simultaneously without the need for metabolic or chemical isotopic labelling. In this presentation we will present some highlights from these studies, focusing on the commonalities of the biological responses observed in these and other studies. We will also discuss statistical validation of protein expression changes, including recent work on the development of a procedure for estimation of false discovery at the protein quantitation level.