Proteomic Strategies for the Identification of Proteins in Durum Wheat

Although the fulfillment of genome sequences of several green plants has not yet been completed, there are many researches focused on the determination of the functional network of proteins by proteome analysis. In the last decade, a wide identification of proteins by MS was performed in rice, Arabidopsis, maize, barrel medic (Medicago truncatula) The relatively small genome size of rice (420 Mb) and its importance as a food grain have made rice a primary target for genome sequencing and proteomic studies. On the contrary, proteomic studies in wheat are in progress and the database of wheat is incomplete also owing to the large genome size (16,000 Mb). In a recent work, to broaden the knowledge of the durum wheat gluten proteome, three cultivars were compared in two different growing seasons by a proteomic approach. Most of the wheat proteins are very difficult to identify because they have homologous sequences to other proteins. For that reasons, new proteomic approaches have to be developed for the study of these wheat proteins. In this work, two different enzymatic digestion methods and bioinformatics approaches coupled with nanoLC and electrospray ionization ion trap mass spectrometry is described for the identification of metabolic and gluten proteins of durum wheat cultivars, in order to increase the final number of identified proteins. The use of MS techniques in combination with the Swissprot, NCBI and EST Viridiplantae databases allowed us to identify wheat proteins minimizing the risk of false-positive identifications.