Abstract: Systems, device and methods are provided for determining a reference clock frequency for use by a multi-protocol analyzer in connection with a multi-protocol communications system. Initially, the clock frequencies for each of the links in the multi-protocol communications system are determined. The link clock frequencies are then used as a basis for determining the frequency of the reference clock. While the reference clock frequency is based upon the link clock frequencies, the reference clock frequency is different from each of the reference clock frequencies.