How to determine whether a protocol is l2tp or not?

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The protocol overview in RFC2661 should give you an idea of the relationship between the various protocols. As for your first question, the identification of an L2TP packet is based on the underlying transport. For instance, with UDP transport the UDP port number 1701 is assigned for L2TP payloads. As for your second question, PPP LCP packets are part of, you guessed it, PPP. How the PPP frames are carried, either over L2TP or otherwise (e.g. PPPoE) does not matter. So the answer would be: PPP LCP may or may not be L2TP payloads, but are not part of L2TP itself.