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Suppose we have some equipment made by a manufacturer that digitally records and measures some data and communicates it with a PC. They haven't provided any documentation on the protocols it uses for communicating this data with the PC nor does it seem that they intend to ever.

Now, we have been able to figure out the sequence of bytes through reverse engineering and have been considering producing some equipment that augments the data by performing calculations and sending control sequences back to the initial equipment.

The protocols are proprietary with regards to them being developed by company X for the purpose of operating company X's machinery via PCs running proprietary software.

Can our idea be brought to market as add-ons to company X's equipment without infringing on anybody's patents or intellectual rights?

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To figure out whether your proposed product would infringe anyone's patents, you would have to review all the relevant patents. A good starting place would be looking at the granted patents assigned to company X, but it's possible that there are relevant patents held by others as well.

Other intellectual property rights are outside the scope of this site, but you might be able to get information about those from Law.SE. There may be some copyright attached to the control sequences, but that's far from my area of expertise.

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