I think most mass spec or proteomics or -omics studies go 1 or 2 main ways. You're focused on understanding a biological system at some important granular level or you are building a resource for people who are.
ImmPRes is a really beautiful new(?) [they've been working on it for 8 years, but the web portal is new to me, so I think that counts as new(?)] example of the latter, born from years of experiments in the former.
http://immpres.co.uk/ let's anyone interested in the proteomes of immune cells to easily dig through data on all sorts of cells associated with the human/mammalian systems.
For example, say you're interested in just CD4 cells --
Now....I know that we're supposed to do hypothesis driven research...but how often does that come up in explorative -omics? I'm impressed when it does, but most is "how the fuck does this system work?" and I really think that is where most of us operate these days. If you can get to a point where you've got a resource easy enough for anyone to dig through, you've done something good for the world in my clearly exceptionally biased opinion.
You can read a little bit more about ImmPRes here.