Most HP/Agilent mass spectrometers have power outlets on the back of the mass spec in order for you to plug your rough pump(s) into. In this case, the software can accommodate automatic "Pump Down" and "Vent" procedures. This is a great idea for a new mass spec, or a new mass spec owner/operator.
Two ways to connect power to your rough pump.
1. Connect the power cord to the back of the MSD like the manufacturer intended you to do.
2. For older mass specs, especially ones that need frequent service, and operators that are familiar with the vacuum theory of mass spectrometers - I prefer another means. I prefer to plug the rough pump(s) directly into a wall socket and control the "on/off" manually. In this case, I can leave the rough vacuum on during times when I wish to shut down the mass spec for an extended period. I can have the rough pump on an entirely different electrical circuit (breaker) and it will still be running in the case of a power overload of the mass spec, or mass spec circuit breaker. And, my most favorite reason - I can leave the rough vacuum on while doing an electronics "reset" of the mass spectrometer.