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, N2 or He, 1-2 mL/min
• Injector
• Oven
• Column
• Detector
 Syringe

Injector
Detector

Gas tank

Column

Oven
 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)
Syringe Syringe

Injector Injector

He
He

Purge valve
closed Purge valve
GC column GC column open
 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
Open Tubular Capillary Column

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

15-60 m in length
 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 C18:2
C18:1

C16:1 C18:0

Polar column RT (min)

C18:2

C18:1
C16:0

C16:1 C18:0

RT (min)
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
220C

160C

50C

0 60
Time (min)
 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 (107)
• 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
EI Source
Under high vacuum
filament

70 eV e-

To mass
analyzer

GC column

anode
repeller Acceleration
slits
 EI process
• M + e- M+*

f1 f2 f4
f3
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
RT: 14.48 - 24.30
RT: 20.82 NL: 9.69E5
AA: 3547389 TIC F: {0,0} + c EI
BP: 67 det=350.00 Full
100
ms [
95 25.00-510.00]
MS ICIS evanssaf
90

85

80

75

70

65
R e la tive Abu nd ance

60

55

50

45

40

35

30 RT: 21.04
AA: 665791
25
BP: 55
RT: 16.04
20 AA: 304398 RT: 21.90
BP: 74 AA: 291543
15
RT: 16.84 BP: 28
10 AA: 78898
BP: 28
5

0
15 16 17 18 19 20 21 22 23 24
Time (min)
 CI/ ion-molecule reaction
• 2CH4 + e-  CH5+ and C2H5+

• CH5+ + M  MH+ + CH4

• 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/m/z
• Unit resolution for quad and trap
• TOF up to 15000
• FT-ICR over 30000
– MALDI, Resolve 13C 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
 594.3 MVVTLIHPIAMDDGLR
594.7
Q-TOF C78H135N21O22S2+3
595.0
601.3
595.3 601.7
601.0
602.0

m/z
901.4
100

95

90 LCQ 891.7
85

80
891.2
75

70
R = 0.88 902.3
65

60
892.6
55

50

900.6
45

40

35

30

25

20

15

10

m/z
Quadrupole Mass Ion Filter
Ion Trap
Time of Flight -TOF
Where:
•mi = mass of analyte ion
•zi = charge on analyte ion
•E = extraction field
•ti = time-of-flight of ion
•ls = length of the source
•ld = 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)
• C9H15NO4, FM 201.1001 (mono-isotopic)
• Mass accuracy = {(Mass Error)/FM}*10 6
• Mass Error = (5 ppm)(201.1001)/10 6 =
 0.0010 amu