The aim of this work was to study the effects of Fe and Mn deficiencies and Mn toxicity on the protein profile of the xylem sap of tomato (Solanum lycopersicum), with the aim of elucidating plant response mechanisms to these nutritional stresses. Tomato was chosen as a model plant because the tomato genome has been published and this plant species has adequate root pressure and turgid stems that permit xylem sap sampling in sufficient amounts by de-topping. The high-throughput shotgun analysis has permitted to identify and quantitate a large number of low abundance proteins in the tomato xylem sap.