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My initial though was to clock the scope with one of the signals in the differential pair. This, of course, means that jitter will not be measurable since the scope will always trigger on the rising (or falling) edge of the signal, effectively not displaying the jitter.
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I need to correct myself. Jitter is defined as variations in the high or low bit times and due to this, the jitter will be visible as variations in the signal transitions in the right part of the eye diagram. Therefore, it should be fine to trigger the scope on one of the differential signals. It will not be accordingly to the PCIe spec's compliance rules but it will be useful as a comparison tool to find out whether signal degradation occurs in my setup.
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