How To Pump Down (Start) the GC/MSD - EI - MassHunter

Document created by carlos_vargas Employee on Aug 12, 2020Last modified by carlos_vargas Employee on Oct 7, 2020
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This Information Applies To: Agilent 5977B GC/MSD with MassHunter GC/MS Acquisition Software



This article describes the procedure to safely pump down (start) 5977B GC/MSD with Electron Ionization (EI) 


Steps to follow:

Before you turn on the MSD:

  • The vent valve should be open slightly.
  • All other vacuum seals and fittings must be in place and fastened correctly. The front side plate screw should not be tightened, unless hazardous carrier, JetClean system hydrogen, or reagent gases are being used.
  • The GC/MSD interface extends into the GC oven, and a conditioned capillary column is installed in the GC inlet and in the GC/MSD interface.
  • The GC is on, but the heated zones for the GC/MSD interface, the GC inlet, and the oven are off.
  • Carrier gas of at least 99.9995% purity is plumbed to the GC with the recommended traps. The regulator, plumbing, traps, EPC module, inlet, and column have been purged of any gas to remove oxygen from the system.
  • If hydrogen is used as carrier gas, or JetClean system supply, the hydrogen supply shutoff valves must be closed, and the analyzer top sideplate thumbscrew must be loosely fastened.
  • The foreline pump exhaust is properly vented.


Pump Down Procedure:

  • Remove the analyzer window cover and open the analyzer cover.

Remove Covers


  • Verify that the vent valve is open (about 45 degrees counterclockwise from the fully closed position)

Do not open the vent valve without verifying that the JetClean system hydrogen supply shutoff valve is closed if the optional JetClean system is installed. See the Agilent JetClean Operating Manual for warnings regarding hydrogen safety when the hydrogen shutoff valve is open.

  • Plug the MSD power cord into a grounded building’s main receptacle.
  • Press lightly on the side board and hold to ensure a correct seal.
  • Turn on the MSD by pressing the On/Off switch on the front of the MSD.
  • Close the vent valve when it makes a hissing sound.
  • Keep holding the side board.
Pump Down
  • The foreline pump will make a gurgling noise. This noise should stop within a minute, then you can release the side board.

If the noise continues, there is a large air leak in your system, probably at the side plate seal, the interface column nut, or the vent valve. Vent the system and fix the leaks before pumping down again.

  • Start the Agilent MassHunter GC/MS Acquisition software.
  • In the Instrument Control view, from the Instrument menu, select MS Vacuum Control to display the Vacuum Control dialog.
  • Click Pump Down in the Vacuum Control dialog, and follow the system prompts.
  • When prompted, turn on the GC/MSD interface heater and GC oven. Click OK when you have done so.


Vacuum Control - Pump Down


  • The software will turn on the ion source and mass filter (quadrupole) heaters. The temperature setpoints are stored in the current tune (*.u) file.
  • Reinstall the analyzer window cover and close the analyzer cover.
  • After the message "Okay to run" appears, wait 2 hours for the MSD to reach thermal equilibrium. Data acquired before the MSD has reached thermal equilibrium may not be reproducible.
  • If using the JetClean system, prepare the hydrogen system for use. See the Agilent JetClean Operating Manual for warnings regarding hydrogen safety.


Learn more on how to effectively troubleshoot your Agilent 5977B GC/MSD:

GCMS-5977-1270r - Agilent 5977B GC/MSD Diagnostics and Troubleshooting     e-Learning course on Agilent University 

GCMS-5977-2261e - Using Diagnostic Tools to Detect Leaks in Your Agilent GC/MS SQ System    e-Learning course on Agilent University



Keywords: GCMS, 5977B, SQ, MSD, single quadrupole, vacuum, turn on GCMS


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