Virtual 2-DE images from Coomassie (A)- and silver-stained (B) gels of M. truncatula root tissues. Circled and numbered spots correspond to those showing changes between genotypes or treatments (additional files 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13). Spots assigned to more than one number, correspond to differences observed in more than one of the conditions compared. Molecular mass (on the left) and pI (on the top) were calculated using the PD-Quest software and standard molecular weight markers. Spots commonly observed in both staining methods display a subscript lowercase letter: the same letter in the virtual 2-DE image from Coomassie- and silver-stained gels mean that they have the same relative mobility on the gels.