Gas Chromatography-Mass Spectrometry

Function

• Separation of volatile organic compounds

• Volatile – when heated, VOCs undergo a phase transition into intact gas-phase species
• Separation occurs as a result of unique equilibria established between the solutes and the
stationary phase (the GC column)
• An inert carrier gas carries the solutes through the column, the mobile phase

Components

• Carrier Gas, N2 or He, 1-2 mL/min

• Injector
• Oven
• Column
• Detector

Manual or Syringe
Autosampler

Injector
Detector
Purge Valve Various Types
Gas tank

He gas
Column

Oven

Injector

• A GC syringe penetrates a septum to inject sample into the vaporization chamber

• Instant vaporization of the sample, 280 °C
• Carrier gas transports the sample into the head of the column (we use helium)
• Purge valve controls the fraction of sample that enters the column

GC-MS Lecture Supplement Organic Chemistry II

 • Usually operated in split mode unless sample limited

Syringe Syringe

For our samples we will

Injector Injector use a 100:1 split ratio;
thus, most of your
sample will not go onto
the column.

Purge valve
closed Purge valve
open

The Column

• Use fused silica open tubular capillary column (FCOT)

• Use a long column; capillary allows this
• Separation is based on the vapor pressure and polarity of the components.
• Within a homologous series (alkanes, alcohol, olefins, fatty acids) retention time increases
with chain length (or molecular weight)
• Polar columns retain polar compounds to a greater extent than non-polar compounds
(recall: “like dissolves like”)

Fused Silica Open Tubular Capillary Column

0.32 mm ID
Mobile phase
(Helium)
flowing at 1 Liquid
mL/min Stationary
0.1-5
phase
µ

15-60 m in length

GC-MS Lecture Supplement Organic Chemistry II

Example: C16/C18 saturated vs. C16/C18 unsaturated methyl esters

C16:0 C18:2 These are methyl

C18:1
esters of fatty acids.
The first number
indicates the number
C16:1 C18:0
of carbon atoms in
the fatty acid; the
RT (min) second number
Polar column
indicates the number
of double bonds
C18:2 present.

C18:1
C16:0

C16:1 C18:0

RT (min)
Non-polar column

• With polar column, larger molecule has longer retention time; more polar molecule within
a series has longer retention time
• With non-polar column, the higher molecular weight components have the longer retention
time (i.e., C18 > C16), but now the more polar component of a series comes off the column
first, since the less polar component interacts more effectively with the non-polar column.

The Oven

• Programmable
• Isothermal- run at one constant temperature
• Temperature programming - Start at low temperature and gradually ramp to higher
temperature. This leads to:

Features Associated with Temperature Programming

1)

2)

3)

4)

GC-MS Lecture Supplement Organic Chemistry II

Detectors

• Flame Ionization Detectors (FID)

• Mass Spectrometry with Electron Impact (EI)
• Mass Spectrometry with Chemical Ionization (CI)
• Chemical Ionization: “soft” ionization, used to reduce fragmentation of the M+ peak so M+
can be easily observed
• We will focus on mass spec with EI

Mass Selective Detectors

• Recall what we get from mass spec: molecular weight (M+), molecular formula
(M+1/M+2), structural information from fragmentations
• Volatiles: Probe/electron impact (EI),Chemical ionization (CI) or GC/EI,CI
• Non-volatiles (e.g., cholesterol): Direct inlet probe; by-pass GC and insert directly into
mass spectrometer

Electron Impact

• Gas-phase molecules enter source through heated probe or GC column

• 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible
way to form a collection of fragment ions
• EI spectra can be matched to library standards: NIST/EPA/NIH Mass Spectral Library
• http://webbook.nist.gov/chemistry/

Quadrupole Mass Ion Filter

• Eckerd’s GC-MS uses a quadrupole mass ion filter as the mass selective detector
• Note there are four poles in the detector, hence the name

GC-MS Lecture Supplement Organic Chemistry II

Ion Chromatogram of Safflower Oil

• Obtain different peaks for different compounds; each has a unique retention time
• Can obtain quantitative information from chromatogram
• Each peak has a mass spectrum associated with it.
R T: 14.48 - 24.30
R T: 20 .8 2 N L: 9.6 9E 5
AA: 354 738 9 TIC F: {0,0} + c E I
BP : 67 d et=35 0.00 Full
1 00
ms [
95 2 5.00-51 0.00]
MS IC IS evan s s a f
90

85

80

75

70

65
Relative Abundance

60

55

50

45

40

35

30 R T: 2 1.0 4
AA: 66 579 1
25 B P: 5 5
R T: 16 .0 4
20 AA: 304 398 R T: 21.90
BP : 74 AA: 2 915 43
15 R T: 1 6.84 BP : 28
10 AA: 78 898
B P: 2 8
5

0
15 16 17 18 19 20 21 22 23 24
Tim e (m in )

Using the NIST Library

• Compare mass spec of peaks in sample with those in NIST Library

GC-MS Lecture Supplement Organic Chemistry II