The document discusses common ionization techniques used in mass spectrometry including electron ionization (EI), chemical ionization (CI), atmospheric pressure chemical ionization (APCI), and electrospray ionization (ESI). EI uses electrons from a heated filament to directly ionize gas phase analytes, often fragmenting molecules. CI ionizes analytes through gas molecule reactions. APCI and ESI occur at atmospheric pressure and can ionize more polar and thermally labile compounds in liquid spray. Each technique has advantages for different analyte properties and phases.

1. Commonly used ionizations techniques
in mass spectrometry
‫ميحرلا نمحرلا هللا مسب‬
EI
CI
APCI
ESI
A. Prof. Sherif M. Taha
Tel: 01004724944
sherif2taha@gmail.com

2. Electron ionization
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Direct ionization
Low to nonpolar analyte
Analyte (gas) react with electrons
(Heated filament, tungestin or rhenium)
Emitted electrons of 70 ev
Hard ionization
(ionized molecules being fragmented too)
O.D.S. J. THROCK WATSON, Introduction to mass spectrometry, (2019)

3. Electron ionization
Increasing sensitivity (ionization)
Repeller (+ ve) push the produced analyte s ions
Electrons being under helical motion (Lorentz force)
Ion extraction and focusing were accomplished
using several accelerating voltages lenses
70 ev
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sudden breakdown of vacuum minimize the lifetime of the filament.
EI works at a high a vacuum that minimizing ion collisions (increase mean free
path) but swap more than 99.99 % of the neutal analyte molecules before its ionization.

4. Electron ionization
EI uses emitted electrons accelerated by 70 ev
To minimize the energy fluctuation effect of emitted electrons And use the available huge mass spectra libraries.
Least tight electrons are emitted first, the rest
of molecule ion energy leads to fragmentation
Attain 14 ev being ionized
Emit thermal e (1 ev)
react again with new M
J.H. Gross, Mass spectrometry Mass spectrometry, 2016
O.D.S. J. THROCK WATSON, Introduction to mass spectrometry, (2019)
O.D.S. J. THROCK WATSON, Introduction to mass spectrometry, (2019)

5. Electron ionization
GC MS/MS 7000, QCAP Egypt
M+
N
Cl
Cl Cl
OP(OCH2CH3)2
S
M-HCl, 2CH2CH3
M-HCl, CH2CH3
M-HCl,
M-HCl, PS, 2CH2CH3
70 ev

6. Electron ionization
GC MS/MS 7000, QCAP Egypt
Molecular ion beak
(m/z = M+) z= 1
Base Beak
70 ev

7. Electron ionization
https://doi.org/10.1016/J.JCHROMB.2020.122106

8. Electron ionization
Ion focus lens
Entrance lens
Repeller
Draw out
Filament New
+ve M
The new produced positive ions pushed by Repeller
And pulled by draw out plate, cylinder.
Main dirty parts of EI source
( more than 6 months injection of herbs samples for pesticides residue analysis ,QCAP Egypt)
https://www.agilent.com/cs/library/usermanuals/public/G7077-90006.pdf

9. Chemical ionization
A higher E of
Emitted electrons
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Indirect ionization
Analytes & ionized gas
molecule reactions.
In presence a reagent gas
of a higher pressure
(higher No. of gas molecules )
Note reagent gas minimize the lifetime of the filament
J.H. Gross, Mass spectrometry Mass spectrometry, 2016

10. Chemical ionization
Analyte ionization by its reaction with gas molecules
𝑀 + 𝐶𝐻4+.
-------------< 𝑀𝐻+
+ CH3
J.H. Gross, Mass spectrometry Mass spectrometry, 2016
O.D.S. J. THROCK WATSON, Introduction to mass spectrometry, (2019)

11. Negative Chemical Ionization
Chromatograms of 50 ng/ml Malathion analyzed by GC–NCI-MS and GC–EI-MS in
SIM mode at right and left respectively.
R. Huˇskova,Analysis of pesticide residues by fast gas chromatography in combination with chemical ionization mass spectrometry, Journal of Chromatography A (2009) 6326–6334
NCI EI

12. Atmospheric pressure ionization (Electrospray ionization)
ESI
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Polar analytes
Analyte in a solution (liquid spray) moves
through electrode and subsequent transformed
into gaseous ions
(Referred as ESI interface)
A pressure transit state
(Atmospheric pressure to vacuum)
Soft ionization
(Thermal labile molecules, smaller and larger polar molecules e.g.
proteins, inorganics)

13. Atmospheric pressure ionization (Electrospray ionization)
ESI main requirements
• Designs (Spraying/ analyzer entrance) that minimize
contamination on the entrance as possible (non volatiles
depositions on the analyzers entrance).
• Electrostatic spraying;
A solution (containing analytes) pass though a needle connected
to high voltage.
MassSpectrometryReviews,2001,20,362–387
+ Ve (mainly) and -Ve ions production
Collecting only + Ve ions, positive ESI
mode. Reverse at Ve ionization mode
Differential pumping across several stages
Vacuum
Jurgen

14. Atmospheric pressure ionization (Electrospray ionization)
Spraying/ analyzer entrance design,
Z shape
https://www.manualslib.com/manual/1782075/Waters-Xevo-Tq-S.html?page=25#manual
Waters

15. Atmospheric pressure ionization (Electrospray ionization)
chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://www.agilent.com/cs/library/slidepresentation/Public/Introduction%20to%20LCMS.pdf
Agilent
Spraying/ analyzer entrance design
Orthogonal

16. Atmospheric pressure ionization (Electrospray ionization)
Spraying/ analyzer entrance design
https://link.springer.com/article/10.1007/s13361-018-2047-2
Bruker
https://analyticalscience.wiley.com/do/10.1002/gitlab.10102/

17. Atmospheric pressure ionization (Electrospray ionization)
Spraying/ analyzer entrance design,
Orthogonal
API 4000™ LC/MS/MS System Hardware Manual
Electrode,
analyte solution spray
Nebulizer
Gas
Nebulizer
Gas

18. Atmospheric pressure ionization (Electrospray ionization)
Spray is directed
away from orifice
Probe
Electrode
Turbo heater Turbo heater
Electrode adjustment cap
Retaining ring
X-axis
Y-axis
Exhaust
SCIEX, Turbo V™ ESI
API LC/MS/MS Turbo Ion Spray, Manual
Turbo V™ Ion Source Operator Guide

19. Atmospheric pressure ionization (Electrospray ionization)
Pneumatic assistance;
- As nebulizer surrounding the needle of
the solution exit.
- Fast desolvation using heated gas on
the sprayed droplets.
Countercurrent gas (Curtain gas);
- Minimize the produced ion clusters
(from non complete desolvation),
prevent/minimize the entrance of air,
solvent, nonpolar matrices towards mass
analysers.
Declustering potential (DP);
- Minimize ion clusters that produced during the entrance in to the vacuum stages (after the orifice) as a result of the
cooling effect by reducing the ion motion. such cooling favor ion aggregation together or forming clusters with
solvents.
- DP (voltage at orifice) should be high enough to prevent ion clusters formation after the orifice and below a level that
cause ion fragmentation.
Turbo V ion Source, AB Sciex™
Electrode,
analyte solution spray
Nebulizer
Gas
Nebulizer
Gas
Desolvation and declustering (inert gas, N2)

20. Atmospheric pressure ionization (Electrospray ionization)
Turbo V™ Ion Source Operator Guide
API LC/MS/MS TurboIonSpray Ion Source Manual
• The mobile phase
1:1 water: acetonitrile
• ISV: Positive mode 4000 to 5500 V.
Negative mode usually lower
-3000 to - 4500 V.
• For too high ISV, a blue glow can be seen
at the tip of the electrode, Turbo Ion Spray,
that may decreases the sensitivity.
• Curtain Gas flow should be as high
as possible. Start at 20 for ABI sciex 4000
and 4500 & 25 for 5000 and 5500
& 30 for 6500

21. Atmospheric pressure Chemical Ionization (APCI)
Chemical ionization at the atmospheric pressure improves the sensitivity
As it increase ion formation by increased analyte reaction with gas ions.
Positive ion
production
Negative ion production (especially
analytes containing carpoxylic acids, phenols)
Both produced simultaneously, It is a matter of lenses polarities
Adducts
Air
https://doi.org/10.1002/jms.1784
Turbo V™ Ion Source operator guide

22. Atmospheric pressure ionization (Electrospray ionization)
Possible ionizations
1.0073
J. Throck, Introduction to Mass Spectrometry Instrumentation, John Wiley & Sons Ltd, England (2007)

23. ESI ionization
TIC of +Q3: from Sample 92 (Boscalid_0.10_SCan_Q3) of 131114_Boscalid.wiff (Turbo Spray IonDrive) Max. 1.1e10 cps.
0 2 4 6 8 10 12 14 16 18 20 22 24 26
Time, min
0.00
1.00e9
2.00e9
3.00e9
4.00e9
5.00e9
6.00e9
7.00e9
8.00e9
9.00e9
1.00e10
1.10e10
I
n
t
e
n
s
i
t
y
,
c
p
s
20.37
22.96
21.37
23.30
24.34 27.86
26.30
20.03
19.62
18.16
17.42
16.38
15.51
0.04
0.73 14.43
13.45
1.49 2.26 12.39
2.99 11.47
+Q3: 20.074 to 20.651 min from Sample 92 (Boscalid_0.10_SCan_Q3) of 131114_Boscalid.wiff (Turbo Spray IonDrive), Centroided Max. 7.0e8 cps.
335.0 336.0 337.0 338.0 339.0 340.0 341.0 342.0 343.0 344.0 345.0 346.0 347.0 348.0 349.0 350.0
m/z, Da
0.0
5.0e7
1.0e8
1.5e8
2.0e8
2.5e8
3.0e8
3.5e8
4.0e8
4.5e8
5.0e8
I
n
t
e
n
s
i
t
y
,
c
p
s
343.0
345.0
346.9
346.1
344.0
341.2 348.0
339.1
335.1 337.1 349.1
338.2
336.2 340.2
N
O
N
H
Cl
Cl
342
342+ 1

24. ESI ionization
TIC of -Q3: from Sample 5 (Boscalid_Only_Coverd15M_) of 131121_Boscalid.wiff (Turbo Spray IonDrive) Max. 4.9e7 cps.
0 2 4 6 8 10 12 14 16 18 20 22 24 26
Time, min
0.0
5.0e6
1.0e7
1.5e7
2.0e7
2.5e7
3.0e7
3.5e7
4.0e7
4.5e7
4.9e7
I
n
t
e
n
s
i
t
y
,
c
p
s
20.21
1.23 21.16
1.87 21.65
23.15
22.24
2.65 3.87 24.56
4.39 5.19 6.02 27.40
26.90
6.75
12.80 14.46 14.83
11.59 17.49
11.17 15.76
8.26 10.04 18.18
-Q3: 20.224 min from Sample 5 (Boscalid_Only_Coverd15M_) of 131121_Boscalid.wiff (Turbo Spray IonDrive), Centroided Max. 1.8e7 cps.
333.0 334.0 335.0 336.0 337.0 338.0 339.0 340.0 341.0 342.0 343.0 344.0 345.0 346.0 347.0 348.0 349.0 350.0
m/z, Da
0.0
2.0e6
4.0e6
6.0e6
8.0e6
1.0e7
1.2e7
1.4e7
1.6e7
1.8e7
I
n
t
e
n
s
i
t
y
,
c
p
s
340.9
342.9
341.8 343.8 344.9
346.0
N
O
N
H
Cl
Cl
342
342- 1

25. ESI ionization
https://doi.org/10.1016/J.JCHROMB.2020.122106

26. Atmospheric pressure ESI and CI
Sciex, The DuoSpray™ Source Rapid switch LC-MS/MS and GC-MS/MS

27. EI CI APCI (API) ESI (API)
Type Hard, direct Soft, indirect Soft, indirect Soft, indirect
Vacuum High Moderate Atmospheric Atmospheric
Source of ionization Filament, e of 70 ev Filament, e of 200 ev A corona by Electrode, 4-5 kv A solution passing
through an electrode
of 3-5 KV.
Analyte phase Gas Gas Gas or liquid spray liquid spray
Analyte polarity Non polar moderate polar Moderate polar and polar Polar and highly polar
Charges one one one One and multiple
Commonly used ionizations techniques in mass spectrometry

28. A. Prof. Sherif M. Taha
Tel: 01004724944
sherif2taha@gmail.com