using an agilent 6890 gcms with entech canister sampler

TEXAS A&M UNIVERSITY KINGSVILLE

Using the Agilent 6890N

GC/MS for Sampling

Volatile Organic

Compounds Using the Entech Preconcentrator

Don Marek

5/30/2014

This is a user guide to the Agilent 6890N GC/MS in Lab 225. This document provides some simplified

instructions to sampling for VOC’s and analyzing with the Entech and Agilent equipment.

Agilent 6890N/Entech Preconcentrator

1

Contents

GC/MS Concepts ............................................................................................................................ 2

Introduction ................................................................................................................................. 2

Compendium Method TO – 15 ................................................................................................... 2

Canisters ...................................................................................................................................... 2

Preconcentration ......................................................................................................................... 2

GC/MS ........................................................................................................................................ 3

Mass Analysis ............................................................................................................................. 4

What are Mass Spectra? (“Molecular Fingerprints”).................................................................. 5

Auto-tuning and Manually Tuning the GC/MS .............................................................................. 6

Adjusting the Peak Widths.............................................................................................................. 8

Microscale Purge and Trap/ Pre-concentration ............................................................................. 10

Standard Operation Procedure for Canister Cleaning ................................................................... 12

Standard Operation Procedure for Standards Preparation Purging the Regulator ........................ 13

Internal Standard Preparation ....................................................................................................... 14


2

GC/MS Concepts

Introduction

The Analytical tools of Gas Chromatography with Mass Spectrometry Detection (GC/MS) will be used to identify the Volatile Organic Carbons (VOC). The USEPA Compendium method TO- 15 will be followed in the sample collection and analysis of the ambient air samples.

Compendium Method TO – 15

The analytical strategy of Compendium Method TO -15 involves using a high resolution GC coupled to a mass spectrometer. Mass spectra for the individual peaks in the total ion chromatogram are examined with respect to fragmentation pattern of ions corresponding to various VOCs including the intensity of primary and secondary ions. The fragmentation pattern is compared with stored spectra taken under similar condition in order to identify the component. For any given compound, the intensity of the primary fragment is compared with the system response to the primary fragment for known amounts of the compound. This establishes the compound concentration that exists in the sample.

Canisters

The canisters used to collect the ambient air samples are made of stainless steel and coated with silonite. The canisters are 6 Liters in volume and are evacuated to a vacuum of 50 militorr. A picture of the canister is shown in Figure 1 below. When the valve to the can is opened, the air passes through a flow restrictor which is an orifice that restricts the flow rate into the can. A diaphragm below the flow restrictor, regulates the flow into the can so that the flow of air at a fixed rate.

Preconcentration

The air sample from the canister is directed to a pre-concentrator which traps the VOCs and remove much of the excess air in the sample. Additionally the pre-concentrator has a purge and trap to remove water vapor from the sample. The sample is desorbed off the trap and carried off with Helium into the GC column for separation.


3

Figure 1: Stainless Steel Silonite Canister

GC/MS

GC/MS is the combination of two powerful analytical techniques. Gas chromatography is the physical separation of two or more compounds based on their volatility from the liquid phase to the gas phase. The gas chromatograph employs a carrier gas (mobile phase) to move a sample in the vapor phase through a column coated with a stationary phase where separation takes place. A detector converts the column eluent to an electrical signal that is measured and recorded. The output of the GC is a plot of detector signal abundance versus time. The abundance remains at a low “baseline” level except when a separated sample component elutes from the column and produces a peak in the chromatogram plots. Chromatographic peaks can be identified from their corresponding retention times measured from the time of sample injection to the time of the peak maximum. The retention time of any component peak is unaffected by the presence of other


4

sample components. The height of the area of a peak may be used to measure the concentration of a component in the sample mixture.

Mass Analysis

A mass spectrometer is one kind of GC detector. As the separated sample component molecules elute from the column to the inside of the MS, they are bombarded with energy. This is to remove an electron from them and converts them into unipositive ions. Some chemical bonds may also break up in this process and the resulting fragments may rearrange or break up again to form more stable fragments. A mass spectrum is a recording of the masses of each of the ionized fragments, representing a unique fingerprint of a molecule that can be used in identification.

Figure 2 : Typical GC/MS System.

As shown in Figure above, the sample is separated into its components by the column mounted inside the gas chromatograph. The components are then ionized and identified by their characteristic spectra produced by the mass spectrometer.

1. Gas supply: Typically Helium though due to cost and shortage other gases can be substituted depending upon application.

2. Pneumatic Controls: Control flow and pressure of gases into the GC. Refer to manual for guidance.

3. Injector: Where the sample is injected. This may be manual or with an auto-sampler.

4. GC Oven: The temperature of the GC oven can be programmed to optimize separation and resolution of the components of a given sample. Precise temperature control of the oven allows the chromatography to be reproducible.


5

5. GC Column: The column separates the mixture into its components.

6. Interface: The interface between the GC and MS must transfer the sample / carrier gas

matrix from positive pressure inside the MS. It must reliably transmit the entire sample without compromising the performance of the GC or the MS.

7. Ion Source: In the electron impact (EI) ion source, a filament wire emits electrons that strike the sample molecule as they elute from the column. Ions are produced from the electron/molecule collisions and a series of lenses propels and focuses them toward the quadrupole.

8. Mass Analyser/Quadrapole: The quadrapole consists of four conductive rods, separates ionized fragments according to their mass/charge ratio. Voltage on the rods can be set to allow ions of a particular mass to pass through and ions of the “wrong” mass will be pumped away by the vacuum system.

9. Detector: The detector counts the ions that pass through the quadrapole. This signal is

small and must be amplified. An electron multiplier detector measures the abundance of each component ion, and the presence of an ion is ultimately recorded as a mass peak in a mass spectrum.

10. Vacuum System: The MS operates under a vacuum of about 10-5

torr. The reduced pressure increases the distance between the molecules, minimizing the number of intermolecular collisions inside the ion source.

11. Control Electronics: The data system is responsible for the total control of the GC/MS

system. This includes GC temperatures, tuning the MS system, controlling the voltages on the quadruple during the data acquisition, detecting the abundance of each ion, and processing the acquired data.

What are Mass Spectra? (“Molecular Fingerprints”)

A mass spectrum is a plot showing the mass/charge ratio (in atomic mass units or amu) versus abundance data for ions from the sample molecule and its fragments. The charge of ions formed in the GC/MC is +1 and the mass / charge ratio of any fragment is therefore normally equal to the mass for that fragment. The largest peak in the spectrum is called the BASE PEAK.

Certain fragments are more prone to form from the parent molecule than others, due to the presence of functional groups in the molecule and their interconnection. The masses of these fragments are used to deduce the structure of the parent compound. The ionized parent molecule, when seen as part of the mass spectrum, is referred to as MOLECULAR ION.

The mass spectra of certain compounds exhibit cluster of mass peaks. These clusters represent “naturally occurring impurities” or isotopes that are present for carbon, nitrogen, sulfur, chlorine,


6

bromine, and a few other elements. The relative percentage of these cluster ions provides more clues useful in identifying a parent molecule from its molecular fingerprints.

Auto-tuning and Manually Tuning the GC/MS

Before samples can be analyzed using the GC/MS, the mass spectrometer must be tuned. Each day that the instrument is used, the performance of the MS shall be checked. The performance check only needs to be performed once per day.

The parameters for passing an Autotune are as follows:

The three tuning masses in the upper profile part of the report shall be within +/- 0.2 amu of 69.00, 219.00, and 502.00. The peak widths of these three peaks shall be 0.60 +/- 0.1 amu.

The peak at 69 amu shall be set to 100 % relative abundance

Relative to the peak at 69 amu, the peak at 219 amu shall be in the range of 70-250 %.

Relative to the peak at 69 amu, the peak at 502 amu shall be greater than 3 %.

Relative to the peak at 69 amu, the peak at 70 amu shall be in the range of 0.5-1.6 %. Relative to the peak at 219 amu, the peak at 220 amu shall be in the range of 3.2-5.4 %.

Relative to the peak at 502 amu, the peak at 503 amu shall be in the range of 7.9-12.3 %.

M/z 28 greater than m/z 18 may indicate an air leak somewhere in the system.

If an air leak is detected, the air leak shall be isolated and corrected.

The instrument shall be tuned again.

.

The MS is tuned by adjusting several parameters while the Per-fluoro tributylamine (PFTBA)is injected to the MS chamber. Below is the procedure for tuning the GC/MS:

1. Click on the icon to start the Chemstation software. 2. From the “View” menu select “Manual Tune”.


7

3. When prompted “be sure changes are saved. Switch View Now?”, select “Yes” 4. In the “Manual Tune” view select the “AdjParam” menu to adjust the tune parameters. 5. From The “AdjParam” menu select “Edit MS Params” menu 6. From the ”edit MS Params” menu select “Scan” and you should see a similar PTFBA

spectra a s shown in Figure 2-1. Wait 30 seconds for the PFTBA levels to stabilize before changing any tune parameters.

The scan from 10-700 amu should have less than 200 peaks. If there are more than 200 peaks then some sort of contamination is entering the MS chamber and further trouble shooting should be done. The mass spectrum of PFTBA has a base peak of 69 amu. The relative abundance of the mass peak of 219 to the base peak in the PTFBA spectra should be between 40 and 85%. The relative abundance of the mass peak of 502 to the base peak in the PTFBA spectra should be between 2.5 and 5%. In the “mass” column in Figure 2-1, if the masses of 69, 219, and 502 are off by more than 0.2amu then the mass axis should be adjusted. This is done by selecting “Mass Axis” from the calibrate menu. By doing this the mass axis is automatically adjusted by the software. The “Rel Abund” column shows the relative abundance of the 69, 219, and 502 masses. To adjust the relative abundance, the EN lens and the EntLens offset parameters should


8

be adjusted. The Entrance lens parameters are inversely proportional to the relative abundance, which means that if you wish to increase the relative abundance you should lower the entrance lens setting and vise versa. The abundance of mass 69 should be between 200,000 and 400,000. To adjust the abundance the EM volts parameter should be adjusted. The EM volts are directly proportional to the abundance. An increase in the EM volts parameter will increase the abundance. Click on the “Prof” button to get a profile of the 69, 219, and 502 peaks. The profiles are shown in Figure 2-2. The peak with at 50% of the peak height (Pw50) should be between 0.57- 0.63

Adjusting the Peak Widths

To adjust the peak widths the amu gain and the amu off set parameters should be adjusted. The relationship between the peak widths and the amu gain and the AMU off set are shown in the following figure. In order to increase the peak width the amu gain and the amu off set parameters should be decreased, and vice versa to decrease the peak width.

Figure 3 : Relationship between peak width and AMU gain and AMU offset.


9

After changing the tune parameters print the parameter settings by selecting “print” from the file menu.

Click on “OK” to leave the edit Parameters view.

Save the tune values by selecting “save tune values” from the file menu. Save the file as ATUNE.U.

Select “Top” from the view menu, to switch to the top view. When Prompted “be sure changes are saved. Switch View Now?”, select “Yes” Note, if changes have not been saved go ahead and do so now other wise the changes will be lost once the view has been switched.

After the mass spectrometer has been tuned then a sequence table will be prepared to run the samples using the AAVOC1 method. The instrument parameters for the GC/MS-FID system are shown in the table below:

Column DB-1. 60m long, 0.32mm OD, 1 micron coating Gas Pro, 30m long, 0.32mmOD

Flow Rate He; 1.3 ml/min Mode: Splitless Injector Temperature 150° C MS Transfer Interface 280° C FID Settings Temperature: 250° C

Hydrogen flow: 40 ml/min Air flow: 450 ml/min Make up gas flow: 45 ml/min

MS Settings Scan range: 35 – 200 atomic mass units Scan Rate: 4.3 scans per second Solvent delay: 4.17 min MS Source: 230°C MS Quad: 150°C

Temperature Program Initial oven temperature: 20°C Initial hold time: 2.7 First ramp: 2.76 C/min Next temp: 90°C Hold: 0 min Second ramp: 10.90 C/min Next temp: 130°C Hold: 0 min Third ramp: 6.18 C/min Next temp: 220°C Hold: 18 min Total Run Time: 64.3


10

Microscale Purge and Trap/ Pre-concentration

In order to avoid interferences of the MS results, the air, carbon dioxide and water must be removed from the sample. These components are removed with the Entech 7100a preconcentrator. In Module 1 (M1) of the pre-concentrator the VOC’s are trapped onto glass beads while all gases more volatile than methane, which include carbon dioxide and air, are allowed to pass through. Module 2 (M2) of the pre-concentrator contains a sorbent material called TenaxÒ which absorbs the water from the sample. In Module 3 (M3), the focusing module, the VOC’s in the sample are liquefied and then quickly vaporized, and injected into the GC transfer line. A schematic diagram of the pre-concentrator is shown in the figure below. The settings for the pre-concentrator are shown in the tables below.

Figure 4 : Schematic Diagram of the Pre-concentrator.


11

1. Connect the canisters to the sample ports. Make the connections finger tight first, then tighten with a wrench.

2. Click on the NT 7000.exe icon to open the Entec Pre-concentrator Software.

3. Enter the sample names in the same order as the sample log table for the GC/MS

4. The internal standard volume for all samples, will be set at 20 ml.

5. After entering the sample name click on the sample port that the can is connected to.

6. Enter the sample volume of 400 ml.

7. Enter “C:\Smart\tceq4.mpt” as the method.

8. Click on the add icon to add the sample to the sequence table.

9. After all the samples have been added to the sequence table, click on the leak icon to leak check the connections to the canisters. It is important that there are no leaks otherwise air from the lab can dilute the sample drawn into the pre-concentrator. Make sure that all the canister valves are closed before leak checking.

10. Click “Go” to start the leak check. The leak check fails if the initial pressure is not the same as the final pressure. If a sample port fails, undo the connection, reconnect, re-tighten, and leak check again.

11. After all sample ports pass the leak check, click on the green “Go” Icon. Make sure that all canister valves are open before pressing “Go”.


12

Standard Operation Procedure for Canister Cleaning

After the sample has been analyzed by the GC/MS the 6L canisters are cleaned for reuse. The canisters are cleaned by flushing the canisters with humidified zero grade air, evacuating the canister to 0.2 psia with a rough pump, and further evacuating the canister to 100 militorr. The flushing and evacuations are repeated for four cycles. In the final evacuation the canisters are evacuated to 50 militorr. During the flushing/evacuation cycles heating bands heat the canisters to vaporize any condensation along the canister walls.

1. Make sure the cylinder pressure of the zero grade air is above 500 psig. If the Pressure is below 500 psig, replace the zero grade air cylinder with a new one. Make sure the line pressure is at 50 psig.

2. Make sure that the water level of canister cleaner is between 80-20%. If the water

level is below 20% then HPLC grade water needs to be added. Before removing the humidifying vessel from the canister cleaner be sure to close the valve to the zero grade air cylinder. Fill the humidifying vessel with HPLC grade water till the level is 80% full.

3. Re connect the humidifying vessel to the can cleaner. Open the valve to the zero

grade air cylinder. Check for an air leak on the nut of the humidifying vessel. Spray the nut with a 50/50 mixture of methanol and water. If the bubbles form at the nut, then tighten the nut until the leak stops.

4. Wrap the heating bands around the can. Turn on the power strip which the heating

bands are plugged into.

5. Connect can to Canister Cleaner. Tighten the nuts by hand first. Then tighten them with a 9/16” wrench. Make sure the valves to the canisters are closed.

6. Open the software to control the canister cleaner by clicking on the canister

cleaner icon.

7. Click on “Open” and select canclean.m30 to load the set points for the method.

8. Click on “Run” to get to the run control screen.


13

9. Before the can cleaning process is started, the connection of the canisters to the canister cleaner must be leak checked. Click on the rough pump button wait till the pressure of the system is approximately 0.1 psia.

10. Click on the all off button. The system should be able to maintain a vacuum for 1

minute. If the pressure increases by 0.1 psi during this time then there is a leak in the system. If there is a leak in the system, trouble shooting will need to be done to identify the leak If the pressure of the system does not increase during the 1 minute, then the leak check has passed.

11. Open the valves to the cans.

12. Click on the “Go” Icon to start the can cleaning process.

13. After the cans have gone through 4 cleaning cycles and final evacuation. Close

the valves to the can. Hit the all off button. Turn off the power to the heating bans.

Standard Operation Procedure for Standards Preparation Purging the

Regulator

There are three standards, which are the Internal Standard, the 4-Bromofluro-Benzene (BFB) and the Ozone Precursor Mix. Each standard cylinder has a regulator. When a new standard cylinder is received the regulator must be flushed with the new standard to remove pockets of lab air in the regulator.

1. The cylinder valve on the cylinder should be open the regulator valve should be closed.

The needle valve to the cylinder should be closed.

2. Connect the cylinder to the canister cleaner.

3. Perform a manual leak check of the system. Click on the rough pump button wait till the pressure of the system is approximately 0.1 psia.

4. Click on the all off button. The system should be able to maintain a vacuum for 1 minute. If the pressure increases by 0.1 psi during this time then there is a leak in the system. If there is a leak in the system, troubleshooting will need to be done to identify the leak If


14

the pressure of the system does not increase during the 1 minute, then the leak check has passed.

5. Close the regulator valve on the regulator.

6. Open the needle valve to the cylinder.

7. Click on the rough pump button and evacuate the system to about 0.1 psia.

8. Click on the all off button.

9. Open the regulator valve on the regulator slowly till the gauge on the regulator reads about -5 psig.

10. Close the needle valve to the cylinder.

11. Click in the rough pump button and evacuate the system to about 0.1 psia.

12. Click on the all off button

13. Open the needle valve to the cylinder to allow some gas to flow through. The gauge on the regulator should increase to -5 psig.

14. Repeat steps 9-12 six times to flush the regulator.

Internal Standard Preparation

The Internal standard does not need any dilution, however the standard must transferred from the cylinder into a six liter canister. A diagram of how the cylinder, canister and canister cleaner should be connected is shown in the figure below.

1. The cylinder valve on the cylinder should be open the regulator valve should be closed. The needle valve to the cylinder should be closed.

2. Connect the cylinder, and the canister to the tee as show in figure 1. Connect the tee to the canister cleaner system.

3. Perform a manual leak check of the system. Click on the rough pump button wait till the pressure of the system is approximately 0.1 psia.


15

4. Click on the all off button. The system should be able to maintain a vacuum for 1 minute. If the pressure increases by 0.1 psi during this time then there is a leak in the system. If there is a leak in the system, troubleshooting will need to be done to identify the leak. If the pressure of the system does not increase during the 1 minute, then the leak check has passed.

5. Click on the High Vacuum button. Wait till the system is evacuated to 25 militorr.

6. Click on the all off button

7. Close the needle valve to the canister cleaner.

8. Open the needle valve to the cylinder.

9. Open the regulator valve slowly till the line pressure is 35 psig

10. Open the valve to the evacuated canister. Wait till the line pressure returns to 35 psig.

11. Close the valve to the canister.

12. Close the needle to the cylinder.

13. Close the regulator valve.

Figure 5 : Diagram for the internal standard prepration.


16

using an agilent 6890 gcms with entech canister sampler

Environment