This involves two separate questions. Of course, the short answer to both is to discuss this with a patent attorney. But in any case…
How can I protest this patent?
This is still a patent application. It is not yet a patent which can be enforced, and may never become one. Only time will tell.
If you have published the details of your system before the priority date of this application (which is 8 October 2012), this may be prior art which could prevent this application being granted. This can be provided to the examiner as third party observations. The examiner will then consider using your publication in the examination procedure. There are some intricacies in this, which are detailed in MPEP § 1134.
How can I protect myself from being sued by the applicant for infringement?
If the application is granted (and therefore could be enforced), you may be able to rely on the prior user defence.
35 USC § 273 provides:
A person shall be entitled to a defense under section 282(b) with respect to subject matter consisting of a process, or consisting of a machine, manufacture, or composition of matter used in a manufacturing or other commercial process, that would otherwise infringe a claimed invention being asserted against the person if—
(1) such person, acting in good faith, commercially used the subject matter in the United States, either in connection with an internal commercial use or an actual arm’s length sale or other arm’s length commercial transfer of a useful end result of such commercial use; and
(2) such commercial use occurred at least 1 year before the earlier of either—
(A) the effective filing date of the claimed invention; or
(B) the date on which the claimed invention was disclosed to the public in a manner that qualified for the exception from prior art under section 102(b).
Basically, if you used the invention in the US commercially, and that use happened 1 year before the effective filing date of the patent application (which is 8 October 2012), you have a defence to infringement.
To prepare for this, you should get together proof that you used the system several years ago.