Quite simply, is the TPD6F003 a good ESD/EMI protection circuit for JTAG? It won't affect speed or cause a problem?
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As easy as it is, I'd say it can't hurt. That chip is not only ESD 61000-4-2 compliant, but also serves as a pi EMI filter. We did go ahead and use it in our current prototype and our Spectrum Digital XDS100v3 has had no problems communicating that I can see, been using it for several months now.
It might depend on the structure of your product. Will the JTAG connection have a port to the outside where a user could touch it? Then ESD protection is a good idea. Is it outside of any metal shield enclosure that you are using for EMI? And even if so or if not, you still could pick up some radiated susceptibility issues that a simple EMI filter could solve. It's also connected directly to your high speed processor, so the other side of the pi filter could help reduce emissions.
Additionally, ESD may not be enough. Our customer ran our unit through several EMC tests, and we unfortunately did not notice the need for EFT (electrically fast transient) and surge protection on our first pass (protection against external power switch transients, cable connect/disconnect, and nearby lightning strikes). You would need to get some 61000-4-4 and 61000-4-5 rated TVP diodes. TI doesn't seem to have a lot of parts that meet these, though Littlefuse has a wide selection. In extreme cases, you might want a varistor, fuse, and TBU (transient blocking unit) combo to handle even higher surges and shorted wire cases (the fuse protects against the varistor catching fire for extended time shorts). Except for the combination MOV (metal oxide varistors) and a safety fuse, these parts can be very small surface mount and pretty low cost, certainly cheaper than having to reorder new boards and all the engineering rework if you don't pass ESD and EMI.
Another aspect is will you be doing real-time debugging on a unit while it is connected to high power hardware? Perhaps without the full enclosure in place? Then for the debugging phase you might require some of these protections.
Getting back to the JTAG port, EFT and surge probably aren't something you need to worry about there if the end-user won't have a JTAG cable connected. But I still think ESD and simple EMI susceptibility and emissions filtering is a good idea. The TPD4F003, TPD6F003, and TPD8F003 seem to be a good ESD and EMI fit for JTAG.