Question

What organelles work with proteins in the cell?

Answer 1

Ribosomes.

Explanation:

The question is not very clear. Answer depends on what you are referring to as "work with".
The most sensible explanation to me is that you want to know "what organelle makes proteins?" and that is ribosome,the protein synthesizing factory . It translates information from m-RNA to make proteins.
Other possible question would mean "what organelles work(i.e. do their own job) with(i.e. using) proteins? " and that would be the most of them, chloroplasts,mitochondria etc. have their own proteins to work with (to perform their specific functions)