Recently I have come across datachannel. I would like to integrate two infrastructure to enable webrtc interoperability.
Lync server will provide signalling and presence to help locate lync client and other peer is connected to a IMS application server. The other peer is not a lync client and its a webrtc enabled browser. how will I transfer data by integrating this two infrastructure(Lync and IMS)?
Would be great to have some information on which application layer protocols can be used for transferring datastreams thru the peers that are interoperable?
Unless you're prepared to do a lot of low-level coding and/or high-level hair-pulling, my suspicion is that WebRTC isn't quite ready for a scenario like this one quite yet. There are some folks who have managed to get it working with some servers like Asterisk, and there's supposedly a general purpose SIP client available here: https://code.google.com/p/sipml5/. But from what I hear hanging out on the WebRTC mailing list, folks are having a fair bit of trouble with these integration scenarios. There's certainly nothing that just works out-of-the-box. Lync supports SDP and SIP, but I expect that you'd need to spend a lot of time figuring out how you need to transform the SDP that WebRTC generates before it ever gets to the Lync server.
[Edit 1/28/2013] - Beyond the issues above, the real problem maybe with the codecs that are supported by each platform. Currently, I believe that the only codec supported by WebRTC is Google's VP8, which doesn't appear to be supported natively by Lync. So you'd need a realtime gateway/transcoder sitting between them, translating between H.264 (or whatever protocol Microsoft Lync settles on) and VP8. Assuming you can find a gateway to do that - they may very well exist - I can't imagine it's going to scale very well.