GC and GC-MS

Gas Chromatography
Function
Components
Common uses
Chromatographic resolution
Sensitivity
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
Components
Carrier Gas, N
2
or He, 1-2 mL/min
Injector
Oven
Column
Detector
Gas tank
Oven
Column
Injector
Syringe
Detector
Injector
A GC syringe penetrates a septum to
inject sample into the vaporization camber
Instant vaporization of the sample, 280 C
Carrier gas transports the sample into the
head of the column
Purge valve controls the fraction of sample
that enters the column
Splitless (100:90) vs. Split (100:1)
Injector
Syringe
Injector
Syringe
Purge valve
open
Purge valve
closed
GC column
GC column
He
He
Split or splitless
Usually operated in split mode unless sample
limited
Chromatographic resolution depends upon the
width of the sample plug
In splitless mode the purge valve is close for 30-
60 s, which means the sample plug is 30-60
seconds
As we will see, refocusing to a more narrow
sample plug is possible with temperature
programming
0.32 mm ID
Liquid
Stationary
phase
Mobile phase
(Helium)
flowing at 1
mL/min
Open Tubular Capillary Column
15-60 m in length
0.1-5 mm
FSOT columns
Coated with polymer, crosslinked
Polydimethyl soloxane (non-polar)
Poly(phenylmethyldimethyl) siloxane (10%
phenyl)
Poly(phenylmethyl) siloxane (50% phenyl)
Polyethylene glycol (polar)
Poly(dicyanoallyldimethyl) siloxane
Ploy(trifluoropropyldimethyl) siloxane

Polar vs. nonpolar
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
C18 saturated vs. C18 saturated methyl ester
C16:0
C18:0
C18:1
C18:2
C16:1
C16:0
C18:0
C18:1
C18:2
C16:1
RT (min)
RT (min)
Polar column
Non-polar column
Oven
Programmable
Isothermal- run at one constant
temperature
Temperature programming - Start at low
temperature and gradually ramp to higher
temperature
More constant peak width
Better sensitivity for components that are
retained longer
Much better chromatographic resolution
Peak refocusing at head of column
Typical Temperature Program
Time (min)
0
60
50C
220C
160C
Detectors
Flame Ionization Detectors (FID)
Electron Capture Detectors (ECD)
Electron impact/chemical ionization (EI/CI)
Mass spectrometry
FIDs
Effluent exits column and enters an
air/hydrogen flame
The gas-phase solute is pyrolized to form
electrons and ions
All carbon species are reduced to CH
2
+

ions
These ions collected at an electrode held
above the flame
The current reaching the electrode is
amplified to give the signal
FID
A general detector for organic compounds
Very sensitive (10
-13
g/s)
Linear response (10
7
)
Rugged
Disadvantage: specificity
ECD
Ultra-sensitive detection of halogen-
containing species
Pesticide analysis
Other detectors besides MS
IR
AE

Mass Spectrometry
What kind of info can mass spec
give you?
Molecular weight
Elemental composition (low MW with high
resolution instrument)
Structural info (hard ionization or CID)
How does it work?
Gas-phase ions are separated according
to mass/charge ratio and sequentially
detected
Parts of a Mass Spec
Sample introduction
Source (ion formation)
Mass analyzer (ion sep.) - high vac
Detector (electron multiplier tube)
Sample Introduction/Sources
Volatiles
Probe/electron impact (EI),Chemical ionization (CI)
GC/EI,CI
Involatiles
Direct infusion/electrospray (ESI)
HPLC/ESI
Matrix Assisted Laser Adsorption (MALDI)
Elemental mass spec
Inductively coupled plasma (ICP)
Secondary Ion Mass Spectrometry (SIMS)
surfaces

EI, CI
EI (hard ionization)
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 stds
CI (soft ionization)
Higher pressure of methane leaked into the
source (mtorr)
Reagent ions transfer proton to analyte




To mass
analyzer
filament
70 eV e-
anode
repeller
Acceleration
slits
GC column
EI Source
Under high vacuum
EI process
M + e-
M
+*
f
1
f
2 f
3
f
4
This is a remarkably reproducible process. M
will fragment in the same pattern every time
using a 70 eV electron beam
Ion Chromatogram of Safflower Oil
CI/ ion-molecule reaction
2CH
4
+ e- CH
5
+
and C
2
H
5
+

CH
5
+
+ M MH
+
+ CH
4

The excess energy in MH
+
is the
difference in proton affinities between
methane and M, usually not enough to
give extensive fragmentation
EI spectrum of phenyl acetate
Mass Analyzers
Low resolution
Quadrupole
Ion trap

High resolution
TOF time of flight
Sector instruments (magnet)

Ultra high resolution
ICR ion cyclotron resonance

Resolution
R = m/z/Dm/z
Unit resolution for quad and trap
TOF up to 15000
FT-ICR over 30000
MALDI, Resolve
13
C isotope for a protein that
weighs 30000
Resolve charge states 29 and 30 for a protein
that weighs 30000
High vs low Res ESI
Q-TOF, ICR
complete separation of the isotope peaks of a
+3 charge state peptide
Ion abundances are predictable
Interferences can be recognized and
sometimes eliminated

Ion trap, Quad
Unit resolution
MVVTLIHPIAMDDGLR 594.3
594.7
595.0
601.3
595.3
601.0
601.7
602.0
m/z
C
78
H
135
N
21
O
22
S
2
+3
Q-TOF
901.4
891.7
902.3
900.6
891.2
892.6
LCQ
R = 0.88

m/z
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Quadrupole Mass Ion Filter
Ion Trap
Time of Flight -TOF

Where:
m
i
= mass of analyte ion
z
i
= charge on analyte ion
E = extraction field
t
i
= time-of-flight of ion
l
s
= length of the source
l
d
= length of the field-free drift region
e = electronic charge (1.6022x10-19 C)

TOF with reflectron
http://www.rmjordan.com/tt1.html
Sector instruments
http://www.chem.harvard.edu/mass/tutorials/magnetmovie.html
FT-ICRMS
http://www.colorado.edu/chemistry/chem5
181/MS_FT-ICR_Huffman_Abraham.pdf
Mass accuracy
Mass Error = (5 ppm)(201.1001)/10
6
=
0.0010 amu
201.0991 to 201.1011 (only 1 possibility)
Sector instruments, TOF mass analyzers
How many possibilities with MA = 50
ppm?
with 100 ppm?

Exact Mass Determination
Need Mass Spectrometer with a high
mass accuracy 5 ppm (sector or TOF)
C
9
H
15
NO
4
, FM 201.1001 (mono-isotopic)
Mass accuracy = {(Mass Error)/FM}*10
6
Mass Error = (5 ppm)(201.1001)/10
6
=
0.0010 amu