In collaboration with Mosaiques Diagnostics we can analyse biofluid proteomes for your needs using capillary electrophoresis coupled to mass spectrometry. This equipment is available in our lab. We have ample experience (>40 papers published) with this approach both in human and animal biofluids, mainly urine. Our robust metabolome analysis pipeline using CE-MS has just been published.
Some references proteome analysis
The reference for metabolome analysis and the link the post is here.