Embodiments of this invention include a protocol sensitive visual navigation apparatus, and associated methods, for navigating and relating different protocol levels of a protocol. A test and measurement instrument can include the protocol sensitive visual navigation apparatus, which can facilitate analyzing, searching, and measuring various aspects of the different protocol layers and cross-correlating items from one protocol layer to another protocol layer. The type and characteristics of the analysis is informed by a selected protocol layer. Physical layer signals or events can be correlated to protocol level information, thereby increasing an understanding of the overall protocol and associated protocol layers and events.