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