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Thermo Fisher Scientific

Baking Out the System


  • The system bakeout of the mass spectrometer removes unwanted gases or molecules (collected or remaining) from the high-vacuum region of the instrument.
  • Ions can collide with those gases or molecules resulting in lower overall sensitivity.
  • Thermo Fisher Scientific recommends baking out the instrument if the high vacuum decreases noticeably during routine operation.
  • Bakeout is mandatory after the system has been vented for maintenance or service work in the analyzer region.
  • User should bake out an instrument that has been vented for at least twelve hours (12 hours) before you can start using it again.
  • If the system has vented during a power failure and it not at the correct pressure and you need to use the system within 24 hours, it is necessary to bake out the system to attain the operating vacuum.


Q Exactive GC


Performing the Bakeout

1. In the Tune software window, click the On/Standby button to put the instrument in Off condition.

2. In the Tasks panel of the Tune software window, click the Vacuum / Bakeout button to display the Vacuum / Bakeout. bake out - step 2.png
3. Enter the desired baking duration (in hours) into the spin box. The available range is 4 to 100 hours.  

4. Click Bake out. A dialog box shows the duration of the baking procedure. Click Yes to confirm the message.

bake out - step 4.png

5. The dialog box disappears and the baking procedure starts.

NOTE: The instrument indicates the active bakeout procedure by a flashing Vacuum LED.Additionally, the Tune software displays a corresponding message box.

bake out - step 5.png

6. The baking of the instrument stops after the preset duration. The Vacuum LED keeps flashing until the cooling and stabilization time (of about 3 hours) is finished. Click Stop in the Vacuum / Bakeout window to abort the baking routine before the preset time.

CAUTION: Hot Surface. Touching hot parts of the instrument immediately after a bakeout might cause burns. If you abort a system bakeout, parts of the instrument can be hot. Allow the instrument to cool for at least three hours before you start operating it again.

Additional Information
  • Before you start the bakeout, ensure that the pumps are up and running at their operating speed.
  • If you have just switched on the mass spectrometer, this will take about 10 minutes.
  • To check the pump speed, open the Instrument Status window of the Tune software and expand the Vacuum System node of the Instrument tree.


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