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The Web API only supports JSON serialization and does not contain support for protocol buffers. What kind of performance gains are you trying to make? I might suggest looking into gzip compression to reduce packet size over the network. To my knowledge, protocol buffers are best suited for server to server communication and in the case you have some end-user client consuming data from the Web API this may not be the best approach.
We are consuming PI Web API from a server. Next thing in the list is GZip as you menthined, thanks.