Just Before Shutdown

STEP 1: Perform an autotune (and air and water check for some models) and print
the report.

Shutting Down for a short time – A few minutes to a few hours

STEP 2: Set the Instrument to Vent
STEP 3: When the instrument is ready to vent, power off the GC, MS and the
computer
When Ready to restart the instrument; just power on the GC, computer and follow
pump down procedure

Shutting Down for a few Days

STEP 2: Set the Instrument to Vent
STEP 3: When the instrument is ready to vent, power off the GC, MS and the
computer
STEP 4: Turn off the carrier gas tank
When Ready to restart the instrument; just turn on the carrier gas tank; power on
the GC, computer and follow pump down procedure

Shutting Down for a week or two

STEP 2: Set the Instrument to Vent
STEP 3: When the instrument is ready to vent, power off the GC, MS and the
computer
STEP 4: Loosen the MS column nut and remove the column from the MS transfer
line
STEP 5: Instal a blank column nut (column nut with no-hole ferrule) on to the
transfer line and tighten
STEP 6: Press the Analyzer door shut and power on the MS for about 1 minute
STEP 7: Power off the MS after about 1 minute
STEP 8: Loosely tighten the Analyzer set screws
STEP 9: Turn off the carrier gas tank

When ready to restart, turn the carrier gas tank, power on the GC and computer,
loosen completely the analyser set screws, open the MS vent valve, remove the
blank column nut from the transfer line, reinstall the column into the transfer line;
and follow MS pump down procedure.

Shutting down for an indefinite length of time

STEP 2: Set the Instrument to Vent
STEP 3: When the instrument is ready to vent, power off the GC, MS and the
computer
STEP 4: Loosen the MS column nut and remove the column from the MS transfer
line
STEP 5: Instal a blank column nut (column nut with no-hole ferrule) on to the
transfer line and tighten
STEP 6: Remove the column from the GC inlet; plug both ends of the column and
store appropriately
STEP 7: Press the Analyzer door shut and power on the MS for about 1 minute
STEP 8: Power off the MS after about 1 minute
STEP 9: Loosely tighten the Analyzer set screws
STEP 10: Turn off the carrier gas tank
STEP 11: Instal a column nut and blank ferrule on to the GC inlet
The above Steps will help you shut down your GCMS properly and help to preserve
the critical components in the MS. Do not store a GCMS system fully vented as the
electron multiplier will degrade over time if exposed to air. The electron multiplier is
a consumable part and is usually not covered by warranty or hardware service
contract.

https://community.agilent.com/knowledge/gcms-portal/w/gcms-knowledgebase/
6928/how-to-vent-shut-down-the-gc-msd---ei---masshunter#:~:text=In%20the
%20Instrument%20Control%20view,display%20the%20Vacuum%20Control
%20dialog.&text=Follow%20the%20instructions%20presented%20on,software
%20into%20Instrument%20Control%20view.

Reference:
Agilent Technologies: GCMS Steps to Shut Down, March 2020