Supporting Information

Introducing Students to Gas Chromatography–Mass

Spectrometry Analysis and Determination of Kerosene
Components in a Complex Mixture

by
Giselle Mae M. Pacot, Lyn May Lee, Sung-Tong Chin and Philip J.
Marriott*

Journal of Chemical Education

Australian Centre of Research on Separation Science, School of Chemistry, Monash University,
Wellington Road, Clayton, VIC 3800, Australia
* PJM email: Philip.Marriott@monash.edu

Part A. Suggested format for the laboratory exercise

Part B. Selected results for the standard mixture; TIC and EIC plots

Part C. Selected results for the kerosene sample; TIC and EIC plots

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 PART A. Suggested format for the laboratory exercise

Gas Chromatography – Mass Spectrometry

Learning Objectives
At the end of the activity, the students are able to:
1. Explain the operation of GC-MS;
2. Consider library searching and limitations;
3. Perform simple interpretation of a mass spectrum, noting differences
between compounds with widely varying molecular ion abundance;
4. Perform extracted ion analysis by identifying specific chemical classes
based on characteristic ions;
5. Conduct selected ion monitoring; and
6. Identify chemical classes and specific compounds present in kerosene.

Introduction
Gas chromatography-mass spectrometry (GC-MS) is a laboratory
technique that merges the capabilities of two analytical procedures. GC
separates different components in a mixture based on their partitioning between
a gaseous mobile phase and a stationary phase in a temperature-controlled oven.
After these compounds are ionised and fragmented, an MS then measures the
mass-to-charge ratio (m/z) and the abundance of these resulting gas phase ions.
Once the GC-MS result is obtained, the student will identify each peak in
the total ion chromatogram (TIC). This can be done by referring to the mass
spectrum associated with the peak of interest and then performing a NIST
library search. Further calculations are conducted and data recorded for this
result as indicated in Table 1. Additional information may be obtained from
extraction ion chromatograms (EIC), which show the response to a particular
m/z value.
In the following exercise, the student will subject two different mixtures to
GC-MS analysis using the appropriate methods and analytical conditions. Some
chemical classes and specific compounds will then be identified from the
interpretation of mass spectral results.

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Experimental
GC-MS instrument: Agilent 7000 triple quadrupole GC-MS system (or any QMS
system)
1. Take note of the details of the column installed in the GC-MS.
2. Learn how to use the appropriate software to operate the GC-MS instrument.
3. Learn how to process the data, including library search and obtaining EIC.
4. The GC-MS run parameters are: injection port and detector temperatures of
250 °C; injection split ratio at 50:1 (reduced to 20:1 (gas saver) after 2 min);
DB-5ms column (30 m length x 0.25 mm internal diameter x 0.25 μm film
thickness; Agilent Technologies); constant carrier gas (He) flow rate of 1.5
mL/min; oven temperature program of 50 °C (1 min) to 300 °C (1 min) at a
rate of 15 °C/min; solvent delay of 1 min.
5. Run the standard mixture. Make sure that the full temperature program cycle
is completed.
6. Once the standard mixture run is completed, the kerosene may be analysed
next.
7. While the second run is ongoing, the results from the first run may be
analysed. Open the Agilent MassHunter Qualitative Analysis software, and
select the correct data file. Using the ‘walk chromatogram’ function, select
each peak in turn to look at its mass spectrum. Record the retention time,
proposed peak identity, molecular weight, CAS#, library match score, and 3-4
major (diagnostic) ions; refer to the attached sheet.
8. Once the kerosene sample run is done, open its data file in the same software.
You will notice that because the sample is too complex, the individual peaks
are not fully resolved. Do the necessary interpretations on this sample; refer
to the attached sheet. You are asked to identify 5 different classes of
compounds in the kerosene sample (e.g. n-alkanes). As a hint, you might try
certain extracted ion plots for diagnostic ions associated with different
chemical classes (e.g. m/z 85 for n-alkanes).
9. Based on the major ions in the standard mixture, set up a selected ion
monitoring (SIM) method. For this mode, you can select retention time
windows and then identify the desired ion masses to scan in each window.
Run the standard mixture using this method.

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10. Calculate approximate linear temperature programmed retention indices
for each component in the solvent sample (this is only possible if you had and
have properly identified the n-alkanes present in the sample). Since
temperature programming is done, use the correct formula for calculating
retention indices.

Report
This will include
 a systematic presentation of your data, including filenames and what each
run represents;
 a compilation of analytical conditions;
 a discussion of each chromatogram and representative mass spectrum; and
 a discussion of component identification and classes of components found.

NOTE: You should complete the attached Tables as you progress through the
experiment.

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Name: ____________________________ Filename & directory path for datafile: ____________________________
Data record for GC-MS analysis of standard mixture
Table 1. Results of the full scan of the standard mixture
No tR Proposed peak Molecula Library Library match Diagnostic ions
CAS #
. (min) identity r mass entry # score (%) (m/z)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17

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Name: ____________________________ Filename & directory path for datafile: ____________________________
Data record for GC-SIM MS analysis of standard mixture

Table 2. Parameters selected for SIM Analysis

Target compounds
Windo Start time End time Ions monitored for
(list the peak # from
w (min) (min) this window (m/z)
Table 1)
1
2
3
4
5

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Name: ____________________________ Filename & directory path for datafile: ____________________________
Data record for GC-MS analysis of kerosene sample

Table 3. Chemical classes in kerosene and two representative compounds

Chemical class
(If you found this using Representative compound Molecula Library match
tR (min)
EIC analysis, include name r mass score
the m/z you selected)

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PART B. Selected results for the standard mixture; TIC and EIC
plots

i. Standard Mixture; Full total ion chromatogram (TIC) result

ii. Extracted ion chromatogram (EIC) m/z 85: Selected to show alkanes;
some other compounds are also displayed

iii. EIC m/z 71: Selected to show alkanes; primarily alkanes are displayed
for this ion mass (peaks 2, 4, 9, 15)

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 iv. EIC m/z 77: Displays the aromatic compounds (peaks 5, 6, 7, 8, 11, 12,
13, 14).

v. EIC m/z 105 shows the xylenes (peaks 6, 7), and the compounds with
benzyl group (peaks 12, 13). Comparing the spectra of peaks 12
(benzoic acid methyl ester) and 13 (benzoic acid), it is evident that the
addition of the methyl group results in earlier elution, and improves
the peak shape. The methyl group should make the compound less
polar, and improves its partitioning into the mobile phase.

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PART C. Selected results for the kerosene sample; TIC and EIC
plots

i. Kerosene sample; Full total ion chromatogram (TIC) result

ii. EIC m/z 85: Selected to show alkanes; this will include straight-chain
and branched alkanes. These hydrocarbons are the most abundant in
this sample.

iii. EIC plot for m/z 83 shows the cyclohexyl- and di-substituted
cyclopentyl compounds. Low abundance ion response for saturated
alkanes gives a small response for the straight chain and branched
alkanes.

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 iv. EIC m/z 128 is the dominant ion for naphthalene (M+ ion) (tR ~ 5.95
min), but the low abundance M+ ion for nonane is also selected at this
mass.

v. EIC m/z 142 is the respective strong methylnaphthalenes M+ ion (+

small decane peak)

vi. EIC m/z 156 is the strong dimethylnaphthalene (DMN) M+ ion, but its
low abundance now means that the undecane peak at tR ~ 5.00 min has
similar response. There are many DMN isomers, but MS does not
provide a precise structure assignment.

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 vii. EIC m/z 170 is the respective strong trimethylnaphthalene M+ ion.
Dodecane at tR ~ 6.00 min is now much larger. Additional alkyl
substitution leads to later elution.

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