Proteomics bridges the gap between DNA and proteins. The genome remains unchanged, but the protein expression is modified as genes are turned on and off in response to environmental conditions. Analysis by two dimensional electrophoresis (2DE) combines isoelectric focusing, based on isoelectric point followed by molecular weight separation by sodium dodecyl sulphate gel electrophoresis (SDS-PAGE). Two DE is a powerful tool to identify protein polymorphisms in wheat flours. The aim of this study was to determine the effect of low nitrogen and low phosphorous and a combination of the two on gluten protein expression as measured by proteomics. The South-African standard for spring wheat quality, SST806, was planted in 2 l pots, filled with 2 kg soil in the greenhouse for two consecutive seasons. Four fertilizer treatments were applied to 15 pots per replication in 2016, and 20 pots in 2017, of which one treatment was the optimal control. Low nitrogen and low phosphorous stress and a combination of the two was applied from the three leaf stage using an existing protocol. Mature grains were milled, and gliadins were extracted from the flour and discarded as the study focussed on the high and low molecular weight glutenins. Isoelectric focussing (IEF) was used in the first dimension, followed by SDS-PAGE for the second dimension. SameSpots software was used to identify protein spots that were significantly up- or down regulated due to stress conditions. Preliminary results indicate that low nitrogen had the most pronounced effect on the expression of proteins, followed by a combination of low nitrogen and low phosphorous stress. Specific spots linked to stress response will be identified and sequenced.