A system may include a plurality of subsystems, e.g. instrumentation units housed in separate chassis, each chassis including multiple instrumentation devices, e.g. data acquisition cards. Each subsystem may generate a local reference clock, which may be phase aligned and locked with respect to one or more similar reference clocks of other subsystems, via a high-level precision time protocol (PTP). Each instrumentation device within a given subsystem may generate its own sample clock based on the local reference clock, and may generate its own trigger clock based on its own sample clock. All trigger clocks may be synchronized with respect to each other through a future time event issued using the PTP, and each instrumentation device may then use its trigger clock to synchronize any received trigger pulses, which may also be issued through future time events using the PTP. This results in synchronizing the received triggers across all participating instrumentation devices across all participating subsystems, ensuring that data acquisition is properly synchronized across the multiple subsystems.