Protein expression difference in Drosophila speciation

We aim to determine the difference of protein expression in the closely related Drosophila species D.melanogaster and D.simulans to gain further insight into protein expression profiles of both species. Analysis of the protein levels might hint to pathways that have evolved into different direction and explain the separation of th species from their common ancestors. Further, we try to characterize novel gene isoform by combining RNA sequencing and proteomics.