Electronic measurement instruments have a critical demand for real-time protocol analysis of high-speed interconnect buses. They require high-speed processing capabilities for gigahertz-level signal acquisition and full protocol visibility from the physical layer to the transaction layer in protocol analysis to support high-precision diagnostics with nanosecond-level jitter. However, traditional CPU-based software solutions are constrained by operating system scheduling latency and cache jitter, making low-latency processing challenging. Commercial protocol analyzers are costly and lack embedded flexibility. To address these issues, this article leverages the hardware parallelism and real-time advantages of FPGAs, considering the importance of the PCIe 2.0 protocol in measurement systems, and proposes a full-stack real-time analysis architecture. This architecture aims to break the throughput bottleneck of traditional software solutions while avoiding high costs. In the descrambling part, an advanced prediction pipeline design is proposed to achieve efficient descrambling. The system achieves full protocol coverage from the physical layer to the transaction layer through data preprocessing, parallel decoding, advanced prediction pipeline descrambling, and state machine parsing. Specifically, 128-bit parallel preprocessing accomplishes symbol alignment and data down-sampling, 80-bit processing completes 8b/10b parallel decoding and advanced prediction pipeline descrambling, and three types of dedicated state machine parsers are responsible for protocol field extraction and CRC verification. Experimental results on the Kintex UltraScale series FPGA platform show that the system operates stably at 312.5 MHz, supporting real-time analysis of 5 GT/s line-rate data. The processing latency from input data to detection results is 22 clock cycles (approximately 70 ns). The CRC verification achieves a 100% match rate, with resource utilization of only 1.39% LUTs and 0.24% FFs. The results demonstrate that the proposed architecture meets practical application requirements in terms of latency, resource overhead, and functional completeness.