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Using Protocol Buffers, it is easy to specify fixed data structures and homogeneous vectors like one might find in languages like C++ and Java. It is however, quite another matter to interwork with these languages when requirements call for working with compound structures, arrays of compound structures, or unstructured collections (e.g. bags) of data.
At bottom, a wire-stream is nothing more than a concatenated stream of primitive wire type strings. As long as you can associate a tag with its host type in advance, you will have no difficulty in decoding the message. You do this by supplying the structure. Tell the parser what is possible and let the parser figure it out on its own, one production at a time. An example may be found in the appendix.