How to Bake Out an Agilent GC/MSD

Created by Vincent Nguyen over 2 years ago | Last modified by Carlos Vargas 12 days ago

This Information Applies To: Agilent 5975, and 5977 Series GC/MSD

Issue

After maintenance requiring venting of the GC/MSD such as a GC capillary column change, filament replacement or abrasive ion source cleaning there will be a decreasing chemical background in the MSD after re-establishing high vacuum. The decrease in chemical background can be accelerated to a stable chemical background by a bake out of the MSD analyzer.

Steps to follow

Caution: GC/MSD bake-out must not be used to attempt to fix or find air leaks. Only bake the MSD, if the system is air leak free, baking the system in the presence of air leaks may cause contamination or damage to the ion source.

Prior to bake out ensure that the ion source has been correctly cleaned, correctly assembled and re-installed in the MSD analyzer and the MSD pumped down.

Refer to the following articles:

How to Clean the EI/CI Source in the Agilent 5977A/B

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

Prior to Bake Out, check that the Air and Water Background is acceptable, please review:

How to Check the Air and Water Background in the Agilent 5975 and 5977 GC/MSD

If a significant Air Leak is present review:

Troubleshooting Agilent 5975 and 5977 GC/MS Air Leaks and resolve the air leak.

Click Instrument > GC Parameters > Columns - set the Gas Chromatograph column flow to 1.2 ml/min then Apply and Exit back to the main menu

Figure1. Setting column flow
Click View > Tune and Vacuum Control

Figure 2. Tune and Vacuum Control location
Click Execute> Bake out MSD and then set the following parameters
Source bake temperature: 300 °C
Quad bake temperature: 200 °C
Bake Time: 6 hours (typically 1 to 6 hours)

Figure 3. Bake Out parameters
Click Ok to start the Bake Out cycle. When the bake time finishes, it may take at least one hour for the source and quad to return to the temperatures set in the tune file.