Figure 3.

Composition of peptides identified in the Brunner and Bodenmiller studies. FlyBase residue composition was calculated from Flybase release 5.4. (a) Comparison of the percentage of each amino acid found in the Bodenmiller peptides and in the Drosophila proteome. (b) Comparison of the proportion of each amino acid in the Brunner peptides and the Drosophila proteome. The three sets of proteins differed most in the proportion of hydrophobic and disorder-promoting residues. (c) Comparison of the percentage of each type of residue in five different sets of peptides. Hydrophobic residues were C, F, I, L, M, V, W and Y. Disorder promoting residues (Extreme LDR) were A, D, E, G, P, N and S (according to Romero et al. [35]). BodenDisc is the subset of peptides that could be used to discriminate one isoform from another in the Bodenmiller analysis; BrunnDisc is the subset of peptides that could be used to discriminate one isoform from another in the Brunner analysis. The Brunner discriminating peptides had markedly fewer hydrophobic residues and markedly more disorder promoting residues than the whole set of Brunner peptides and the Drosophila proteome.