ERROR: Not allowed to change setpoint when in MS Shutdown.

Hi ID_HUNTER I moved your post to the GC/MS Forum for better visibility.  Thanks!

When the MSD power is turned on, the foreline pump starts immediately. It must make it down to less than 400 millitorr in less than eight minutes or it will shut down the system. The screen capture above shows the rough vacuum at 442529 mTorr - which is nearly atmospheric pressure. 

To start up:

• Verify that there is carrier gas connected, turned on, and the regulator is set high enough for the GC inlet to function properly - typically 60 to 80 psi.
• The GC is ready to go
• The gas lines, inlet(s), and column(s) are sufficiently purged with carrier gas
• Open the GC oven door and make absolutely sure that a column is installed into the MS with the proper nut and ferrule.
• Loosen both analyzer shipping screws completely. The vacuum holds the analyzer shut, so they are not needed during normal operation.

To Pump Down the MSD in EI Mode

1. Remove the analyzer window cover
2. Open the vent valve by turning the knob counter-clockwise – do not open it too far, ~1/2 turn is sufficient
3. Hold the analyzer door shut. Press on the metal box on the side board.
4. Press the Power button on the front of the MSD
5. The foreline pump will make a gurgling noise.
6. Listen to hear a sucking sound from the vent valve. This signifies that the side plate has sealed. Close the vent valve fully.
7. The rough pump gurgling should stop within a minute.
8. Start MassHunter Data Acquisition
9. In the Instrument Control view of the Instrument menu, select MS Vacuum Control to display the Vacuum Control dialog.
10. Click Pump Down in the Vacuum Control dialog and follow the system prompts
11. When prompted, turn on the GC/MSD interface heater and GC oven. Click on OK when you have done so. The software will turn on the ion source and quadrupole heaters. The temperature setpoints are stored in the current tune file (*.u).
12. After the message Okay to run appears, wait at least 2 hours for the system to reach thermal equilibrium. Data acquired before the system is equilibrated may not be reproducible

Your patience will be rewarded. Take your time to ensure that the vacuum is acceptable before you proceed.
Do not start until the vacuum is less than 6 or 7 x 10-5!