This Information Applies To: 5975 and 5977 GC/MS systems with MassHunter Acquisition software
High-quality GC/MS data requires a low, and stable background of air and water present in the MS analyzer.
This article demonstrates a systematic procedure to diagnose and troubleshoot a higher than normal air background.
Air and Water background will always be present in the GC/MS vacuum system.
Air background is at m/z 28 (Nitrogen) and m/z 32 (Oxygen). The ratio of Nitrogen to Oxygen should be ~ 4:1 representing their relative proportions in ambient air. Water background is at m/z 18.
The following table summarizes the typical relative abundances of the air and water background with no significant leaks in the vacuum system or GC carrier gas system and no Helium carrier gas contamination.
See How to check the Air and Water Background on an Agilent 5975 and 5977 GC/MS to learn how to evaluate the air and water background.
Table 1. Typical Air and Water Background Relative Abundance
Time after pump down and thermal stability
Water m/z 18 Relative Abundance
Nitrogen m/z 28 Relative Abundance
Oxygen m/z 32 Relative Abundance
Steps to follow:
Large Ambient Air Leak
The MS will not achieve high vacuum during pump down and the foreline pump is automatically turned off in about 7 minutes.
1. If the MS does not achieve high vacuum (Turbo Pump >80% Speed or Diffusion Pump Hot), then there must be either a defective foreline vacuum pump, a defective high vacuum pump, or a large ambient air leak. Figure 1 shows the most common sites for large ambient air leaks in the MS, including:
- Vent Valve area - twisted, crimped or cut valve O-ring
- GC/MS Interface Nut area - column not installed, wrong interface column ferrule, reversed orientation of the interface column ferrule, no interface column ferrule, broken column near interface nut / ferrule
- MS side plate vacuum seal area - twisted or stretched O-ring, contaminated O-ring (dust, lint, or hair)
- Foreline pump hose and fittings.
Tips: Review How to Pump Down (Start) the GC/MSD - EI - MassHunter to ensure you are correctly establishing the MS high vacuum (pump down).
Figure 1. Common sites for MS vacuum leaks
2. If the foreline pump has been automatically turned off in about 7 minutes since starting a pump down, the system was not able to achieve either >80% Turbo speed (turbo pump systems) or <300 mtorr foreline vacuum (diffusion pump systems).
A simple test of the foreline pump and vacuum seals is to open the Vent Valve before turning on the system to pump down. Upon turning on the system you should be able to hear the air being sucked in at the vent valve while pressing the analyzer assembly against the side plate O-ring of the vacuum manifold. Then closing the vent valve and continuing to apply pressure to the analyzer for 20 seconds should create enough vacuum that the analyzer assembly can't be pulled away from the vacuum manifold.
If there is no sucking noise at the vent valve, turn off the system and check the foreline hose for damage and the vacuum connections at the foreline pump hose ends. Also check the volume and condition of the foreline pump oil (for rotary vane vacuum pumps).
Check that the foreline pump actually powers on when the system is turned on. Check that the foreline pump is plugged into the foreline pump power outlet at the rear of the MSD and that the separate power switch on the pump itself is in the on position. If these are all Ok and the foreline pump still does not turn on, contact a local Agilent support representative for further support.
Significant Air Leak
The MS will achieve high vacuum but the air and water background levels are higher than the reference values in Table 1.
1. See the article How to check the Air and Water Background on an Agilent 5975 and 5977 GC/MS and work through the Manual Tune method to Step 10.
2. Double click the PFTBA field or slide the PFTBA slider so that the PFTBA calibration valve in now in the Closed (Off) state. Monitor the m/z 10 to m/z 100 background without PFTBA to continue the troubleshooting process.
3. Troubleshoot for the site of the air leak of the MS using a compressed gas while continuing to scan from m/z 10 to m/z 100.
Use Argon (m/z 40), 1,1,1,2-tetrafluroethane (Miller-Stephenson MS-222N Spray Duster or Agilent Duster Aerosol p/n 8500-6460) ( m/z 33, 69, 83), or Butane (m/z 29, 43, 58).
Only use a very gentle stream of the compressed gas for a brief time (1 second) at each potential leak site.
When the compressed gas is applied to the location of the MS leak, the spectrum will change to the compressed gas being used often with a corresponding decrease in the air m/z's within a few seconds. Wait until the spectrum returns to just the air background and again try a brief reapplication of the compressed gas to confirm the leak location.
Remember that if you decide to check the GC column connections and inlet components, the compressed gas used will have a delayed arrival at the MS when testing potential leak sites at the column inlet and further upstream. The delay will be at least the T0 (void time) of the column or longer if the column phase retains the leak testing compressed gas compound (e.g. PLOT, thick film, or volatiles applications columns).
4. Once the site of the MS leak is located the way to resolve the leak should be readily identified with a disassembly and careful inspection of the leak site (e.g. damaged vent valve O-ring and may require a magnifier to see).
5. If no leak site is found in the MS, then consider half-splitting the system by venting and removing the GC capillary column from the GC/MS interface then checking for capillary column outlet flow by inserting the outlet into methanol or isopropanol to check for flow. If there is no flow with normal inlet pressure then the capillary column must be either broken between the inlet and outlet or blocked at the inlet - if broken replace the capillary column and proceed to pump down again. If the capillary column is not broken install a GC/MS interface nut with a no-hole ferrule and re-establishing the high vacuum and operating temperatures(wait at least 1 hour after the high vacuum and MS temperatures have been established).
If the air leak Nitrogen m/z 28 relative to the PFTBA m/z 69 has significantly decreased to <5%, then the likely site of the leak is from the GC - the column connections, inlet fittings, carrier gas purifiers, carrier gas fittings, carrier gas flow and pressure controllers and carrier gas contamination are all possibilities.
Note: Use a Helium leak detector (e.g. Agilent Gas Leak Detector G3388B) on all GC Helium carrier gas supply fittings, control devices, purifiers and GC flow path components as an outward leak of Helium will create an inward leak of air by diffusion at the leak site that will be easily observed in the MS background spectrum.
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