Intrusion Detection System (IDS) is a type of security management for computers connected in a network. IDS monitor the network for security breach to analyze and identify the intruders. Intrusion detection can be further classified as host and network based, this paper provides analysis of Intrusion Detection System (IDS) on the application layer protocols, by allowing packets for Deep Packet Inspection (DPI), intended for selective protocol non-compliance. By using the defence in depth strategy and passing the traffic into a snoop server all the packets are is captured. This paper is limited to OSI layer 7 application protocols and their corresponding port numbers for traffic analysis.