The Prothean beacon downloaded its knowledge into Lt. Commander Shepard on Eden Prime, causing confusing dreams and visions. While the imagery is becoming clearer with time, the meaning of the beacon communication remains elusive.
It has been suggested the Prothean data recording is highly dependent on a certain point of view, what Carl Jung described as the collective unconscious. The "cipher" needed to comprehend the images implanted in Shepard's mind is the cultural knowledge of a Prothean: the archetypes, biological instincts, and common experiences universal to the race. Since the Protheans have been dead for millennia it may be impossible to acquire this "cipher".