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

This Information Applies To: Agilent 5975 and 5977 GC/MSD systems with MassHunter Acquisition software

Issue:

High-quality GC/MS data requires a low, and stable background of air and water present in the MS analyzer. This article describes how to check the air and water background in the Agilent 5977 and 5975 GC/MSD.

Steps to follow:

Introduction:

Air and Water background will always be present in the GC/MS vacuum system. See Figure 1, Figure 2 and Figure 3.

Air and Water background is determined relative to the PFTBA m/z 69 peak abundance. PFTBA m/z 69 peak abundance is typically ~500,000 counts for the tune report after a full autotune of a 5975 or 5977 MS (atune.u).

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 (see Figure 2).

Tips: High Nitrogen relative abundance without the correct 4:1 ratio to Oxygen (too small on Oxygen abundance, see Figure 3) is usually associated with: Air leak in the Helium carrier gas line upstream of the Helium gas purifier that removes Oxygen but lets the Nitrogen pass through. Excess Nitrogen in the Helium carrier gas from less than 99.999% / 5.0 purity Helium. Excess Nitrogen in the Helium carrier gas from a recently installed Helium gas purifier that has not been sufficiently purged with Helium (gas purifiers are supplied containing Nitrogen gas from the manufacturing process).

Figure 1. Typical carrier gas spectrum without leaks.

Figure 2. Example of air leak spectrum.

Figure 3. Helium carrier gas spectrum,  contaminated with Nitrogen.

The following table summarizes the typical relative abundances of the air and water background without significant leaks in the system.

Table 1. Typical Air and Water Background Relative Abundance

Automated Air and Water Check Method

1. From the Instrument Control menu, select View > Tune and Vacuum Control

Check that the tune file is atune.u, otherwise, load the atune.u file ( click File > Load Tune Parameters).

2. From the Tune and Vacuum Control menu, select Tune > Air and Water Check  and wait until the report is generated (see Figure 4). 

Figure 4. Air and water check report.

3. Evaluate the generated report by comparing it to the values in Table 1.

Tips: If the MS has not been recently tuned, and the calibration valve has been closed for more than a few hours, and the air and water values do not match the values in Table 1, do the following: Repeat the air and water check periodically until the relative abundances of water and Nitrogen are stable before deciding to troubleshoot an unacceptable leak.

Manual Tune Method

1. From the Instrument Control menu, select View > Tune and Vacuum Control

Check that the tune file is atune.u if not load the atune.u file ( File > Load Tune Parameters).

2. From the Tune and Vacuum Control menu select Parameters > Manual Tune (see Figure 5).

• Check that the Vacuum pressures and MS temperatures are in the normal operating range for the GC carrier gas flow entering the vacuum system.
• Check that the PFTBA calibration valve is in the Closed (Off) state.

3. Select the Scan tab of the Manual Tune dialog box and set the Scan Mass Range to Low m/z 10 to High m/z 100 also check that the PFTBA is set to Closed in the Parameters section.

 
Figure 5. Manual Tune Scan tab.

4. Click Scan from the Scan tab to start acquiring data (PFTBA off). The filament turns on, and is emitting light through the MS front manifold window.

5. If any abundance in the Low m/z 10 to High m/z 100 Scan is >500,000 counts immediately click Stop and MS Off to stop scanning and turn off the MS. This action protects the ion source and filament from a high background.

To resolve a significant large air leak see  Troubleshooting Agilent 5975 and 5977 GC/MS Air Leaks.

6. Allow the GC/MS ion source and background abundance to stabilize - this may take 30 to 60 seconds (see Figure 6).

 
Figure 6. PFTBA Off Low m/z 10 to High m/z 100 Scan.

7. Click Stop and MS Off to stop scanning and turn off the filament.

8. Double click the PFTBA field or slide the PFTBA slider so that the PFTBA calibration valve in now in the Open (On) state.

9. Click Scan from the Scan tab to start acquiring data (PFTBA On) as shown in Figure 7.

Figure 7. Manual tune scan PFTBA open.

10. Allow the PFTBA m/z 69 abundance to stabilize, it may take >3 minutes if the PFTBA calibration valve has been closed for more than a few hours (see Figure 8).

Tips: With a low air and water background of <5%, subsequently change the Scan Mass Range to Low m/z 10 to High m/z 50 to focus on just the air and water abundances. The m/z 31 (CF+ is a low relative abundance ion from PFTBA) should be larger than m/z 32 from the Oxygen in a low and stable air and water background GC/MS system (see Figure 9).

Figure 8. PFTBA On m/z 10 to m/z 100 Spectrum.

Figure 9. PFTBA On m/z 10 to m/z 50 Spectrum

11. Record the PFTBA m/z 69 abundance plus the water (m/z 18), Nitrogen (m/z 28), and Oxygen (m/z 32), then compare them to the values in Table 1.

12. if the results suggest that there is a significant air leak, see Troubleshooting Agilent 5975 and 5977 GC/MS Air Leaks for the procedure to locate the leak.

Learn how to effectively troubleshoot your Agilent 5977 GC/MSD: Agilent 5977 GC/MSD with MassHunter Workstation e-learning course available from Agilent education.