We still have a "missing protein" issue. Questions like: Is this protein real? The genomics and transcriptomics thinks it is, but do we have mass spectra to back it up? Is there a good reason for why we don't? That kind of thing are still challenging.
This open paper provides great perspective on how we can use the diverse resources of our community to answer these questions!
It's not going to be easy -- but we have all sorts of tools and great scientists out there who may have already solved the question of "is this transcript expressed and where" we just need to bring it all together!