Gas Chromatography Mass Spectrometry:

How to Run Samples through the 7820A

Instrument

Capital Univeristys Chemistry lab hosts two different Gas Chromatography Mass Spectrometry (GCMS) instruments-
the 7820A and the 7890A. Both instruments can be used to identify what an unknown mixture is composed of. The
GCMS is a complicated machine. The user is able to adjust multiple settings, including temperature, amount of material
used and the rate at which the material flows through the machine, in order to achieve the best output. The output is a
chromatogram of various sized peaks as shown in an example in Figure 1. Each individual substance has its own peak.
Thus, if the user is able to obtain the narrowest, clearest peaks, then they can identify the substance. Both GCMS
instruments have a database of hundreds of thousands of substances. Once the user decides that their chromatogram is
as clear as it can be, the peaks can be selected and the database will pull up the substances that best fit what the user
obtained from their sample. GCMS is time- consuming, taking anywhere from 15 minutes to over an hour to run one
sample through the instrument, but the results can be exceptional. Mixtures that contain over 10 different individual
substances can be run through the instrument, and with the right settings, all 10 substances can be accurately identified.

Figure 1 shows an example of the output of a GCMS instrument. Each peak represents a substance that is a part of a
larger mixture.
 Instructions
The instructions provided on the next page are for Capital Universitys 7820A GCMS instrument. The instructions will
not only provide the user with the basics of working this instrument, but also instructions on how to adjust the different
settings to best achieve the results needed for accurate identification of the unknown substances within a mixture. Step-
by- step instructions are accompanied with pictures to help the user find the controls easily and in a short amount of
time- that way multiple runs can be achieved quickly.

Figures
Example chromatograms used are for rapeseed oil runs that are being done by Dr. Clarks Instrumental Chemistry
course over the course of the current semester. Rapeseed oil comes from the plant Brassica napus which is shown in
Figure 2. Rapeseed oil contains around 11 different individual substances. Students in the course are manipulating the
settings on the GCMS to obtain the 11 peaks needed for accurate identification. As settings are adjusted, certain peaks
will appear on the chromatogram- not always all 11 show up. The chromatograms used in the instructions will display
that.

Figure 2 displays the Brassica napus, which can be made into rapeseed oil. Rapeseed oil can be used as a substitute for
olive oil and is used in cooking.
 Instructions for 7820A Gas Chromatography Mass Spectrometry
1. Turn on the Geer Gas Pressure Sources located near the instrument. Consult your professor for the settings
that the gas should be maintained.
2. Turn on the Gas Chromatograph machine. This is done by clicking the power button on the instrument as
shown below.

3. Once the machine is turned on, it will sit idle until the program is opened on the computer. The program will be
titled Agilent GCMS Open Lab. Double click to open and start the program. A green light should shine on
instrument when it connects to the computer program.
4. Once the program is opened it is time to create a method that will be used to run a sample.
a. At the top of the page there is a bar with the words File, Edit, Method, etc. Click on Method
and scroll down to Edit Entire Method
b. Once clicked you will have the option to name and save your method in a folder. Be sure to name
the method accurately so if someone else, or yourself, plans to come back to use this
method it is easy to find.
5. Once the new method is opened the program screen will appear as this.

a. This is the screen that you are going to use to help run your unknown samples.
b. Here we must turn on the oven by clicking the box where it says On. The oven can be left on
whatever default temperature it was last left on.
c. Next, the detector needs to be turned on. Click on the Detectors tab, right next to the Oven tab
and check the box for the front AND back detectors.
6. Once the gas, oven and detector are all on, now you are ready to create a method.
7. Creating a method (this section will go through each of the tabs on the previous figure, what they do
and how you can change the settings on each)
a. Injector determines the amount of your unknown sample that is injected into the machine for testing.
Under this tab you will have the option to wash the needle that takes up sample. This is
recommended so previous samples do not contaminate your own. In the box titled Solvent Washes
put a number between two and five. This is a good amount of washed to ensure your sample will not be
contaminated.

b. Skip Vales and DO NOT change any settings under this tab.
c. Inlet is the part of the column, indicated with a purple line, where the sample is actually injected into the
machine. The temperature of this column should be higher than the highest boiling point of the sample.

d. Column is where the flow and pressure of the sample can be adjusted. Pressure is not changed, but flow
rate is changed. The amount of your sample moving through the instrument will have an effect on the
output, or chromatogram. Flow rates need to run under three milliliters. Too much of a sample
can ruin the instrument.
e. Oven is the most important when running samples through the GCMS. Controlling temperature is your
best bet at obtaining the most accurate chromatogram.
 The max value you can set any temperature at is 350C. Anything above that could ruin the
instrument. The purple box highlights how you are able to change temperature. In this example method,
the user starts the run at 50C and holds that temperature for 2 minutes. Then they increase the
temperature by 40C per minute until the temperature rises from 50C to 200C. Once the
temperature reaches 200C it is held constant for 2 minutes. That is how the table is read and how you
are able to set different temperatures for various lengths of time.
f. No other tabs need to be used or changed. You are ready to save your method
8. To save a method follow these steps. In the top left corner, click File, Save Method As, and remember to
name the method accurately so you or another user is able to understand the method and use it
in the future.
9. Now it is time to run the unknown sample through the GCMS.
10. Your sample will already be in the appropriate vial and once it is

The inlet is a small part on the outside of the instrument. There will be small slots for you to input the glass vial
with your sample in it. If your unknown is the only sample being run, then put it in slot 1.
11. Once your sample is in the inlet you can return to the program on the computer. To run the method you have
created go to the top left corner and click on Run Control, then select Run Method. The machine will now
wash your sample, if you selected that option in step 7a. Then it will take part of your sample, however much
you indicated in the flow rate in step 7d, and inject it into the instrument. The more changes in temperature you
chose in step 7e the longer it will take to run a sample. Unknowns can take anywhere from 15 minutes to 90
minutes.
12. Once the sample is fully run a chromatogram will appear on screen such as this one from Figure 1.

The peaks will NOT be labeled. To view the instruments best matches for which compounds correspond to
each peak you will need to double click on a specific peak. Once clicked another screen will appear and it will
 give you the best matches in percents- form there the user can make an educated guess on what compounds
make up their unknown sample.
13. Before leaving the instrument, the user must start the cool down method. If no one else will be using the
machine right after you, you must set the cool down method. This keeps the machine in an idle
position. This method will already have been created by the professor and can be loaded as follows: In the top
right corner click File, then Load Method and select the Cooldown option. Then click on Run Control,
click on Run Method and the cooldown will begin.

This instruction guide was meant to serve as a starting point to the 7820A Gas Chromatography Mass Spectrometer.
This guide walked step-by-step through the machine itself as well as the many functions the user is able to manipulate in
order to achieve the desired chromatogram. All the settings listed here are on every version of a GCMS. If the user is
able to understand these instructions for the 7820A, they will be able to easily use other versions of a GCMS with ease.
The GCMS is helpful when trying to identify unknown compounds. Its main function is to help scientists take a mixture
of multiple unknown compounds and separate them so they can be identified. Not only do the Capital University
Chemistry students understand the GCMS, but now you can too with this step-by-step guide to GCMS!

References
Agilent Technologies, Inc. Agilent 7820A Gas Chromatograph Operating Guide. Shanghai,
2016. PDF.

Concordia College. Determination of Caffeine in Beverages using SPME-GC-MS. n.d. 8 March

2017.

Masclef, Amedee. Brassica napus. 31 January 2001. painting. 8 March 2017.

Rattray, Chris. When GC Injection Issues Arent Syringe Issues. 9 November 2012. 10 March
2017.

The Hebrew University of Jerusalem . Thermo Polaris Q - An Ion Trap GC/MS. 2009.
<http://departments.agri.huji.ac.il/zabam/Polaris-Q.html>.