GC-MS

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Single Quadruple and Ion Trap

Vacuum System

GC

Ionization
Method

Mass
Analyzer

Detector

Atmosphere

Data
System


Mass Spectrometry

 What is Mass Spectrometry

The basis of MS (mass spectrometry) is the production of
ions that are subsequently separated or filtered according to
their mass-to-charge (m/z) ratio and detected.
The
resulting mass spectrum is a plot of the (relative) abundance
of the produced ions as a function of the m/z ratio.

254.2
100
507.3

%
334.3
194.2
399.7
0

m/z
100

200

300

400

500

600


4S
Sensitivity ()
Speed ()
Specificity ()
Stoichiometry ()
7

HEWLET
PACKAR
T
D

5972A

Mass
Selective
Detecto
r

1.0
DEG/MI
N

HEWLETT
PACKARD

Sample

Gas Chromatograph

Mass Spectrometer (MS)

D C
B
A
Sample

A
B
C

Separation
8

Identification

GC-MS v.s GC
GC-MS

GC-MS
GC-MS
(S/N)

GCMS

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Ionization Methods

Electron Impact

Ionization Methods
CI (NICI; PICI)

Soft

Ionization

EI

Hard
Fragments

No Fragments
Soft ionization gives low fragmentation
Molecular weight determination
Produces theoretical spectra
High sensitivity (low pg levels)
11

EI Spectra from TRACE DSQ

HCB spectra from 2 pg up to 60 ng

Scan EI+
100

2 pg HCB

%
0

71

107

142

214

177

249

284
282
288
253
Scan EI+

100

200 pg HCB

%
0

71

107

142

214

179

249

284
282
288
253
Scan EI+

100

60 ng HCB

%
0
50

71

107
100

142
150

214

177

200

12

249
250

284
282
288
253
300

m/z
350

CIP Spectra
Comparison of EI with PCI using methane and ammonia
Scan EI+
100
% 51

105
77
76 78

182
106

152 181

benzophenone, EI

183
Scan CI+
183

100
%

184

105

benzophenone
methane CI+

211 223

Scan CI+
200

100
%
0
50

183
100

150

201
200

13

benzophenone
ammonia CI+
217
250

300

m/z
350

 Electron Ionization
GCMS

Most common method of ionization for GC-MS
Used as both a qualitative and quanitative tool
Produces mass spectra of molecules
Fragmentation fingerprints
Combine with retention time for positive identification

Use single ion for quantitation with one or more ions for verification

14

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Ionization Methods

Chemical Ionization

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Ionization Methods

Positive Ion Chemical

Ionization

Reagent gas reacts with electrons to form reactive

species

Result is softer ionization which results in primary

formation of molecular ions.

Main use is molecular weight confirmation

17

 PICI Summary

Molecular weight information

Increased selectivity for many compounds

Selectivity affected by reagent gas

CI

High pressure CI produces true CI spectra

(including adduct ions for confirmation)
18

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Ionization Methods

Negative Ion Chemical

Ionization

 NICI

Reagent gas reacts with electrons to form plasma of thermal

electrons

Ionization is favored by molecules which have a high electron

affinity electron capture

Useful for selective analysis in heavy matricies, ie.e pesticide in

food or waste matrix.
20

 NICI Summary

Molecular weight information

Highly sensitive and selective - ideal

for analytes in complex matrices

21

Detector
Electron Multiplier (Most common)
Faraday Cup
Photomultiplier Conversion Dynode
Array Detector
Charge (or Inductive) Detector
22


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 MS Detection

Answers the two most frequently asked questions in

Analytical chemistry IDENTITY

- What is in this sample?

QUANTITY - How much of it is in this sample?

24

 How does an MS detector do this?

MS detectors constantly acquire Mass Spectra

1-5 spectra are acquired per second
i.e. mass range 50-550 amu, scan rate 5 scan/sec,
~ 2500 amu/s
A chromatographic run is defined by thousands of
mass spectra

25

 Chromatograms?

TIC
TIC

100

If we zoom into
this region
...
region...
%

50

Time
Time
1.25

1.50

1.75

2.00

2.25

26

2.50

2.75

3.00

3.25

 Chromatograms close-up

TIC

100

At this scale the trace

is made from many
data points

78

Time
2.12

2.14

2.16

2.18

2.20

2.22

27

2.24

2.26

2.28

 Mass Spectrum
produced by scanning the MS between 50 and 300 amu
whilst compound elutes into the system

240

100

241
0
60

80

100

120

140

160

180

28

200

220

240

260

280

300

 What is a Mass Spectrum?

A mass spectrum is a chemical fingerprint

It contains:
Molecular weight information
Structural information

29


Each position on the chromatogram has a unique mass spectrum

30

Trace produced by summing all observed masses in each scan

Total Ion Chromatogram or TIC

31

Data View - Chromatogram

We can also just show the data for a specific mass
This lets us see only the information from a single compound

32

 Mass chromatogram

240.27
240.27
1.41e5
1.41e5

100
100

%
%

Mass 240

00
TIC
TIC
4.67e5
4.67e5

100
100

%
%

TIC
00

Time
Time
1.40
1.40

1.60
1.60

1.80
1.80

2.00
2.00

2.20
2.20

33

2.40
2.40

2.60
2.60

2.80
2.80

3.00
3.00

Data View - Extracted ion trace

Removes the effect of background

Increases signal to noise
Separates co-eluting peaks

34

Data View - Extracted ion trace

2 closely eluting peaks as
seen on the TIC. But
each peak represents a
different compound with a
different mass spectral
fingerprint.

TIC
1.57e5

100

Time
11.00

35

12.00

Data View - Extracted ion trace

254.2
100
507.3
TIC
1.57e5

100
%
334.3

194.2

399.7

m/z
100

100

200

300

400

500

600
%

194.2

226.2

402.2460.2

580.4

400

600

0
100

200

300

500

m/z

Time
11.00

36

12.00

Separating co-eluting peaks

254.23
5.81e4

100
%
0

194.20
6.14e4

100
%
0

TIC
1.57e5

100
%
0

Time
10.50

11.00

11.50

37

12.00

12.50

Extracted ion traces

Extracted ion traces give better S/N
removing background
Separating co-eluting peaks

Extracted ion traces can also be used for:

PEAK TRACKING
ACCURATE QUANTITATION

38

Peak Tracking
TIC of explosives mixture

100

0.52

TIC
2.21e6

Which one
is HMX?

5.65
5.72
5.59

3.82

5.81
%

4.95

3.25
1.67

4.25
2.00

1.00

2.00

3.00

4.00

39

5.00

6.00

Time

Peak Tracking
Mass spectrum of HMX
84

100

113

89

237

72
59

131

205

106

69

158

0
40

60

80

100

120

140

40

160

180

200

220

240

m/z
260

Peak Tracking

2.00

100

Mass Chromatogram
m/z 237

0
100

0.52
5.65

3.82

5.81

1.672.00

3.25

4.95

TIC

4.25

Time
1.00

2.00

3.00

4.00

5.00

41

6.00

7.00

8.00

9.00

Data View - Options

Total Ion Chromatogram

The best way to view the whole chromatogram and all peaks visible

Extracted Ion Traces

The best way to see data from just one compound

42


m/z
MS Spectrum

SIC (Selected Ion Chromatogram)

TIC (Total Ion Chromatogram)
Retention time

43


SCAN mode

V m/z

SCAN

V650

V50
0.5sec

0.5sec

ime

44


SIM(Selected Ion Monitoring) mode

V m/z
SIM

97

100
85

V97

50

V85
80.0

0.2sec 0.2sec 0.2sec Time

85.0

90.0

95.0

45

100.0

Scan & SIM Mode

SIM
152
72
54

m/z

TIC : Scan Mode

Retention time
46

Summary so far...
MS detectors acquire mass spectra which can be used for: Molecular weight determination
A TIC chromatogram
An extracted ion chromatogram
Improves s/n
Removes matrix
Separates co-eluting peaks

47

GCoven
MS

48

49

50

liner)





51

52





1.()

2.()

53






54

55

56

GC-MS
The world leader in serving science

The World of Mass

Analyzers


Quadrupole
RFDC
amu
Ion Trap

RF

Magnetic Sector

Time of FlightTOF

58

Quadrupole

Ion Source Body

Lens 1 & 2

S
N

Phosphor

PUMP

+ +

-ve Ion Dynode

S
N
Repeller

+ve Ion Dynode

Trap

Prefilters

Source Magnet

GC
59

GC-MS
The world leader in serving science

Single Quadrupole Mass

Analyzers

61

 Quadrupole Arrangement

+/-(U+Vocost)

-/+(U+Vocost)

Ion beam
62

+
+

Ions scanned by varying the DC/RF voltage

across the quadrupoles
DC/RF
63

10

100

500

64

Quadrupole Illustration of Mass Separation

65

 (Scan Mode)
Full Scan
Library Search
SIM (Selected Ion Monitoring)

Sequential Full Scan

SIM events
SIM
66

 Full Scan MS

Q0

Q1

Q1

M/Z

Q0

Q1

67

DETECTOR

Full Scan
R T :

7 9 .9 7

- 8 9 .2 6
N
2
T
9
0
3

8 4 .6 4

1 0 0
9 5

L :
.7 1 E 7
IC F :
M S
3 0 7 0 7 0 4 _
4 0 7 0 8 1 4 4
3 1

9 0
8 3 .6 3

8 5

TIC

8 0
7 5
7 0

Relative Abundance

6 5
6 0
5 5

8 4 .4 9
5 0
4 5
4 0
3 5
3 0

8 5 .6 2

8 6 .3 2
8 5 .9 5

8 7 .8 0

8 7 .3 7

8 7 .1 4
8 3 .4 7

8 8 .1 1

8 8 .5 3

8 8 .8 9

8 6 .7 1

8 5 .2 9

2 5
2 0

8 4 .2 6
8 4 .1 0

1 5
1 0
8 0 .8 1

8 1 .2 4

8 1 .6 1

8 3 .1 6

8 2 .1 9

8 2 .0 6

8 3 .4 0

0
8 0

8 1

8 2

8 3

8 4

8 5
T im e

9 3 0 7 0 7 0 4 _ 0 4 0 7 0 8 1 4 4 3 3 1 # 1 2 9 9 2
T : + c F u ll m s [ 5 0 . 0 0 - 4 0 0 . 0 0 ]

R T :

8 4 .6 5

A V :

N L :

8 6

8 7

8 8

8 9

(m in )

One Click

5 .9 4 E 6
1 7 2 .1

1 0 0
9 5
9 0
8 5
8 0
7 5

Spectrum

Library

7 0
9 8 .1

Relative Abundance

6 5
6 0

Search

5 5
5 0
4 5
4 0
3 5
3 0
2 5
2 0
7 2 .1
1 5

5 6 .0
1 7 3 .2

1 0
8 1 .1
5

7 0 .0
6 9 .1

1 2 8 .0

1 4 4 .1

9 9 .1
1 1 6 .1

8 4 .1

1 4 2 .1

1 5 5 .1

1 7 4 .1

2 0 2 .1

2 2 5 .1

2 4 6 .1

2 6 9 .1

2 8 1 .0

2 9 8 .9

0
6 0

8 0

1 0 0

1 2 0

1 4 0

1 6 0

1 8 0

2 0 0

2 2 0
m

2 4 0
/z

68

2 6 0

2 8 0

3 0 0

3 5 5 .0

3 2 7 .2
3 2 0

3 4 0

3 6 0

3 6 3 .0

3 8 6 .1
3 8 0

4 0 0

 EIC Co-eluting
254.2

TIC
1.57e5

100

100
507.3

%
334.3
194.2
399.7
0

m/z
100

200

300

400

500

600

%
100

194.2

402.2
460.2

226.2

580.4

0
m/z

100

200

300

400

500

Time
11.00

600

69

12.00

 co-eluting peaks
100
%

254.23
5.81e4

Mass 254

100

194.20

Mass 194

6.14e4

%
0

100

TIC

TIC

1.57e5

%
0

Time
10.50

11.00

11.50

70

12.00

12.50

 Improving Sensitivity

Single Ion Monitoring

Multiple Ion Monitoring

71

SIM MIM
SIM

Set quadrupole to pass a single characteristic

ion during a retention time window in the
chromatogram
10100
Increases sensitivity 10-100X

Lose spectral specificity
72

SIM MIM
MIM
25
Monitor 2 to 5 characteristic ions in addition to
SIM quanitiation ion

Set acceptable qualifier ion ratios to confirm
detection

More qualifier ions boost confidence but reduce

sensitivity gains
73

MS/MS

SIM

74


Ions

of all m/z stored until time to detect

External
Ionization
Ion Trap Mass
Analyzer

Step 2 - Ion Ejection

Step 1 - Store Ions
75

 Basic Steps

Ion Trapping

Ion Injection

76

Mass-selective
Ejection

 Scan functions

Full Scan

SIM (Selected Ion Monitoring)

MSn Isolate a parent ion and fragment to

form daughter ions.

77

 Full Scan MS

2. Detect

1. Inject

78

 Single-Ion Monitoring (SIM)

1. Inject

3. Detect

2. Isolate

79

 Isolation of Ions
qz (wo)
Ions at different qz values oscillate at different frequencies
(wo)

qz
0.0

0.908

o
80

q z
2 2

Analytical Benefits of MS/MS

Increased selectivity
Concentration of analyte too low
Chemical interferences too high (complex matrix)

Structural characterization
Provides information about chemical structure of
unknown compounds

Ease of use
Routine GC/MS/MS is as practical as GC/MS
81

 What is Sensitivity?
Sensitivity is a function of the Signal to Noise
Signal/Noise = Sensitivity
To improve Sensitivity
Increase Signal
or
Reduce Noise
82

How we improve Sensitivity

S/N Sensitivity
Quadrupoles use SIM to increase S
Ion trap uses MS/MS to reduce N

83

84

MS/MS
1. Inject

3. Fragment

2. Isolate

4. Detect

85

MS/MS
EI

EI MS/MS

Collisional
Activation Event

Isolation Event

86

MS/MS Analytical Benefits

Increased selectivity

Advantageous when
concentration of analyte is low compared to chemical
interferences (complex matrix)

Structural characterization

Provides information about chemical structure of
unknown compounds

Ease of use
Routine
GC/MS/MS is as practical as GC/MS
87

MS/MS

MS
Less sensitive than MS

Can only analyze for target analytes

88

GC/MS Ion Trap

SIM

MS/MS

(MSn)
Scan
MS/MS

89

Should I sell Single Quadrupole of Ion Traps?

ITQ 1100 GC/MSn

ISQ

90

Table of Contrasts
Ion Traps

Single Quadrupoles

Mass Separation in time

Mass Separation in space

High sensitivity Full Scan

Lower sensitivity Full Scan

Selectivity of MS/MS

High sensitivity SIM

Library Search

91

Outcomes of Contrasts
Ion Traps

Single Quadrupoles

Mass Separation in Time

Mass Separation in Space

Allows for Fast GC

High sensitivity Full Scan

by Trapping over Time

Lower sensitivity Full Scan

High sensitivity SIM
By scanning a single ion
over time

Lower sensitivity SIM

Multiple stages of MS
For Confirmation/
And Structure Elucidation

No multiple stages of MS
92

Thank you
for your attention

93