Are you asking how to identify such a target protein? Well, you could sequence cancer peptides using mass spectrometry, or sequence the cancer cells' genome, and look for proteins that are sufficiently mutated relative to the wild type copy. However, we already have pretty good knowledge of which genes tend to be mutated most often in cancer cells, so you could do targeted sequencing on those genes first to look for low-hanging fruit. In general, it's still a hard problem, though.
