How To Vent (Shut Down) the GC/MSD - EI - MassHunter

Document created by carlos_vargas Employee on Aug 12, 2020Last modified by carlos_vargas Employee on Sep 3, 2020
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Agilent Support Engineer Insights


This Information Applies To: Agilent 5977B GC/MSD with MassHunter GC/MS Acquisition Software



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

The MSD will be damaged by incorrect venting. A diffusion pump will push back upstream vaporized pump fluid onto the analyzer if the MSD is vented before the diffusion pump has fully cooled. The turbo pump will be damaged if it is vented while spinning at more than 50% of its normal operating speed.

Steps to follow: 

Agilent recommends that safe temperatures are applied to the GC, GC/MSD interface and MSD to vent the system. If direct communication (DCOMM or LVDS) with the GC is established, you must predefine a Fast Vent method to use this option. If you do not have direct communication (DCOMM or LVDS) between the GC and MSD, create and save a Vent Method with GC oven, Auxiliary heaters (MSD Transfer Line), and inlets turned on and set at room temperature. 


  • Remove the analyzer window cover.

Remove Analyzer Window Cover

  • In the Instrument Control view, Instrument menu, select MS Vacuum Control to display the Vacuum Control dialog.
  • Click Fast Vent if your system supports direct communication between the GC and MSD, or click Vent if it does not, to begin the vent cycle. 

Vacuum Control  


  • Follow the instructions presented on the screen, and wait until the vent cycle is completed. When the MSD is vented, Do Not put the Agilent MassHunter GC/MS Acquisition software into Instrument Control view. Doing so will turn on the interface heater
  • Close shutoff valves to hydrogen sources that enter the analyzer if the instrument is so equipped.

If hydrogen is used as a carrier gas or JetClean system supply, the carrier and JetClean system supply shutoff valves must be closed before turning off the
MSD power. If the foreline pump is off, hydrogen will accumulate in the MSD and an explosion may occur. Read Agilent GC/MS Hydrogen Safety before
operating the MSD with hydrogen gas.

  • Turn off the MSD by pressing the power switch.
  • Unplug the MSD power chord

Never open the vent valve without first closing the hydrogen supply line to all possible sources of hydrogen entry to the analyzer. This requires closing the hydrogen shutoff valve to the carrier gas flow module and the shutoff valve to the JetClean system supply if either of these hydrogen sources exist on the instrument.


  • Turn the vent valve counterclockwise only 3/4 turns or until you hear the hissing sound of air flowing into the analyzer chamber. Do not turn the valve too far, or the O-ring may fall out of its groove.

Open Vent Valve

Ensure the GC oven and the GC/MSD interface are cool before turning off carrier gas flow to prevent damage to the column.

  • You may now turn off the GC and close all the other gas sources.


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

Agilent 5977 GC/MSD with MassHunter Workstation e-Learning path on Agilent University 



Keywords: GCMS, MSD, SQ, 5977B, Turn off GC/MS


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