rpettingill,
No the Spike software is not capable of measuring phase noise on a pulsed signal. There is no synchronization mechanism built in to software to synchronize to a pulse. Additionally, the measurement duration can be > 1 second depending on what phase noise offsets are selected. You wouldn’t be able to get much resolution on a 5us pulse.
If possible, I would recommend using a CW output on your transmitter, or you would need to roll your own phase noise measurement using our API or trying to capture the pulse in zero-span and post-processing the captured I/Q waveform.
Regards,
Andrew