We have recently initiated a large UK collaboration, funded by a BBSRC sLoLa grant, to characterise the Drosophila embryonic proteome. The project is led by Simon Hubbard (Manchester) and includes Kathryn Lilly, Laurent Gatto & Alfonso Martinez Arias here in Cambridge; Casey Bergman (Manchester), Christine Orengo, David Jones (UCL).
As part of this work we have developed CRISPR-Cas9 based methods for engineering the Drosophila genome in vivo to add isoform-specific tags to specific proteoforms (i.e. see Korona et al J. Dev Bio)
Drosophila Developmental Interactome Project