Label-Free Proteomic Analysis of Five Grapevine (Vitis vinifera L.) Cultivars Under Water Deficit

Previous grape proteomic studies metabolic processes in berries were strongly affected by water deficit in Chardonnay and Cabernet Sauvignon, when assessed with 2D-PAGE. In the present study, five grape cultivars, three red skinned and two white skinned varieties (Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay and Semillon) were exposed to a progressive, seasonal water deficit treatment at the UNR Valley Road Experimental field station, from fruit set until harvest in 2011 to provide a more comprehensive assessment of water deficit effects upon the proteome. The effects of water deficit over time on the abundance of individual proteins in mature grape berry skins were analyzed using nanoflow liquid chromatography – tandem mass spectrometry (nanoLC-MS/MS). For quantitative purposes and without reliance upon isotopic or metabolic labeling, identified proteins were measured by calculating a normalized spectral abundance factor (NSAF) for measuring relative abundance changes between conditions. Two thousand eight hundred and eighty proteins were identified by shotgun proteomics, with 1,210 core proteins quantified in each replicate, variety and treatment. Deficit irrigation induced abundance differences amongst cultivars; however, a common stress response was not shared amongst all five varietals.