This paper presents a summary of experience in developing the deep packet inspection system using full protocol decoding. The paper reviews the challenges encountered during implementation and provides a high-level overview of the solutions to these issues. The challenges can be grouped into two groups. The first group is related to the fundamental tasks which must be addressed when implementing full protocol decoding systems. This includes ensuring correct protocol parsing, which involves identifying and interpreting protocol headers and fields correctly. Moreover, it is necessary to ensure the processing of fragmented packets and the assembly of fragments into the original message. Additionally, the processing and analysis of encrypted traffic is a crucial task that may require the use of specialized algorithms and tools. The second group of problems is related to optimizing the process of full protocol decoding to ensure high-speed traffic processing, as well as supporting new protocols and the ability to add user-defined extensions. While there are open-source systems that address some of the primary issues associated with full protocol decoding, there may be a need for additional effort and specialized solutions to efficiently operate and expand the functionality of such systems. Although implementing deep network traffic analysis tools using full protocol decoding requires the use of advanced hardware and software technologies, the benefits of such analysis are significant. This approach provides a more complete understanding of network traffic patterns and enables more effective detection and prevention of cyber-attacks. It also allows for more accurate monitoring of network performance and the identification of potential bottlenecks or other issues that may impact network efficiency. In this article, we also emphasize the importance of system architecture development and implementation to ensure the successful deployment of deep network traffic analysis tools using full protocol decoding. At last, we conducted an experiment where several advanced optimizations were implemented in the system that had already solved primary issues. These optimizations related to working with memory, based on the features of the traffic processing scheme. By results, we evaluated significant performance improvement in solving secondary tasks, described in this work.