I have an existing system, which is using protobuf-based communication protocol between GUI and server. Now I would like to add some persistence, but at the moment
As mentioned in an answer to a similar question, since v3.1.0 this is a supported feature of ProtocolBuffers. For Java, include the extension module com.google.protobuf:protobuf-java-util and use JsonFormat like so:
JsonFormat.parser().ignoringUnknownFields().merge(json, yourObjectBuilder);
YourObject value = yourObjectBuilder.build();