Aspects of the disclosed technology relate to techniques for protocol analysis during a circuit design verification process. A protocol-specific message capture unit captures messages while or after being transmitted over one or more communication channels between a circuit design model and one or more target devices. A protocol-independent interface unit receives signals carrying the messages and information for processing the messages from the protocol-specific message capture unit. After processing the messages, the protocol-independent interface unit sends the messages to an analysis unit for analyzing the messages based on a protocol file. The analysis unit may then output the messages for displaying.