Ion Sources
Overview of Various Ion Sources
After introducing samples into a mass spectrometer, the next important step is the conversion of
neutral molecules or compounds to gas phase ions. The ions could be molecular or monatomic in
the case of organic or inorganic mass spectrometry respectively. Examples of molecular and
monatomic ions are shown below:
 e
Cu  63Cu 
63
Atomic mass 63
Exact mass 62.93
Figure 1: General representation of ion formation in ions sources.
Ions are needed because their speed and direction of travel can be manipulated by using electric
and/or magnetic fields. This manipulation is crucial to the separation and detection of the chemical
species.
Ions can be formed in a variety of ways. A few examples are presented below (In these examples, M
represents a neutral molecule while the radical or ionic forms of M are indicated with the dot or
charge sign respectively (M, M+ and M-).):
1. ejection of electrons from neutral molecules

e
M 
M   e
2. electron capture
M  e 
 M 
3. protonation
H
M 
M  H 


4. Deprotonation
H
M 
M  H 

5. addition of other cations
 Na
M 
  M  Na 


6. addition of anions
 CH 3COO
M 
 M  CH 3COO 


Devices that are used for the conversion of neutral molecules to molecular ions are called ion
sources. Many types of Ion sources have been developed. Some examples are presented in the list
below:
Table 1. Common ion sources and their acronyms
Ion Source
Electron ionization source
Chemical Ionization source
Matrix Assisted Laser Desorption ionization source
Electrospray Ionization sources
Atmospheric Pressure Chemical Ionization source
Acronym
EI
CI
MALDI
ESI
APCI
Electron ionization Source (EI)
Electron source
-
e-
e-e- ee
e- e e- e
Repeller
Ion Extraction
Lens
To MS
ee- -
ee e- e
eTrap
Sample in
Figure 2: principle of operation of electron ionization ion source
In EI, the sample to be analyzed is vaporized into the ionization chamber by heating. Pressure in the
chamber is typically about 10-5 – 10-6 torr. The neutral molecules (represented by the black circles)
are bombarded by energetic electrons (e-) produced by the electron source which is made from
tungsten or rhenium filament. Typically, an electron is removed from the neutral molecule to form a
radical ion.
Relative Abundance
M  e  M   2e 
100
90
80
70
60
50
40
30
20
10
0
30
40
50
60
70
80
90
100
110
120
130
140
150
160
m/z
Figure 3: The EI mass spectrum of decanol (CH3 (CH2)9OH). Notice the absence of a signal at m/z 158
which is the molecular ion (M+). The base (or tallest peak) is at m/z 42. This is the most stable ion.
This indicates that the initially formed molecular ion fragmented significantly.
For ions to form, the energy of electrons from the filament of the EI must be higher than the
ionization energy of the analyte molecule. Ionization energies of organic molecules are about 10eV
while that of the bombarding electrons is typically 70eV. As a result, the ion that is formed has a lot
of excess energy which causes it to fragment further. The signals observed in the mass spectrum
above (Figure 3) indicate the fragmentation pattern of the molecule. This pattern is often referred
to as the fingerprint of the molecule. The expected molecular ion at m/z 158 is absent because of its
relative instability. It fragmented into other ions whose signals are seen. The most stable fragment is
the one at m/z 42 and this is called the base peak. Due to the extensive fragmentation that occurs in
EI it is classified as a hard ionization source. Advantages and disadvantages of EI are presented in
Table 2.
Table 2. Advantages and disadvantages of electron ionization sources.
Advantages
• Results in reproducible, instrument
transferable, extensive fragmentation
– Information from the mass spectrum
produced with EI can be used to
elucidate the structure of a
molecule.
– This is done by comparing the
spectrum to several spectra in a
Disadvantages
• Analytes must be in gas phase prior to
introduction into the ion source
– This makes it unsuitable for
thermally unstable and non-volatile
compounds
– The non-volatility problem can be
overcome by derivatization of the
analyte to a volatile form (e.g.
•
large database containing spectra of
known compounds. .
Easily interfaced with a gas chromatograph
•
RCOOH can be derivatized to RCOOR
)
Some compounds fragment so extensively
that the molecular ion peak is absent from
their mass spectrum.
– This makes interpretation more
challenging.
Chemical Ionization
Chemical ionization utilizes the same apparatus as EI but it is operated at higher pressure (~ 10 - 100Pa
in the ion box). Also, the electron energy is increased to 200-500 eV so that the electron beam can
penetrate further into the ion box. Chemical ionization is an indirect process. The first step involves
ionization of a reagent gas (such as methane, CH4) with the energetic electrons from the filament
CH 4  e  CH 4  2e   (CH 3  other ions )
In the second step, reagents ions are formed
CH 4  CH 4  CH 5  CH 3
CH 4  CH 3  C2 H 5  H 2
In the third step, the analyte molecule is ionized by reacting with the reagent ions through one or more
of the following reactions:
M  CH 5   M  H   CH 4 (Proton transfer)

M  CH 5   M  CH 5 

(Adduct formation)
M  C2 H 5   M  C2 H 5  (Adduct formation)

M  C2 H 5   M  H   C2 H 6 (Hydride Abstraction)

Besides methane other reagents that are utilized include isobutyl chloride, water, ethanol, acetone, and
methylamine.
Relative Abundance
100
90
80
70
60
50
40
30
20
10
0
30
40
50
60
70
80
90
100
110
120
130
140
150
160
m/z
Figure 4: The CI mass spectrum of decanol (CH3 (CH2)9OH). The peak at m/z 141 is the base peak and it is
due to loss of OH- [M-OH]+. The peak at m/z 157 is the molecular ion peak due to hydride abstraction
[M-H]+.
As noted in the mass spectrum representation in Figure 4, chemical ionization produces less
fragmentation of the molecular ion. As such, the mass spectrum Is simpler and cleaner compared to that
obtained with EI. Additionally, the molecular ion is observed (at [M+H]+ , [M-H]+, and/or [M + adduct]+ ).
However, CI does not produce sufficient fragmentation to facilitate structural information. Additionally,
like EI, it is not suitable for thermally unstable compounds.
Electrospray Ionization Source (ESI)
With ESI, ions are generated under atmospheric pressure. Hence this approach is classified as
atmospheric pressure ionization (API) technique.
The ESI device is comprised of a needle (~ 0.2mm outer diameter, ~0.1mm inner diameter) that is
encased in a sleeve through which a sheath gas flows. This gas (typically N2) is used to nebulize the
sample solution that is pumped through the needle. Sample flow rate is typically about 2 – 500 L /min.
In operation a high voltage (2-6kV relative to the ion extraction cone) is applied to the needle. Ions are
typically formed in solution prior to desorption into the gas phase. To facilitate this, sample solutions are
made in polar solvents such as aqueous methanol or aqueous acetonitrile. The solvent is typically
modified with volatile weak acids such as formic, acetic acids, or trifluoroacetic acid, or salts of weak
bases such as ammonium acetates. This facilitates abundance of charged species ( such as H+) which are
necessary for ion formation.
Upon nebulization, the droplets are surrounded with charged species such as H+. As the droplets
evaporate, the charge density increases. At a certain size, the charge density becomes high enough that
the droplet explodes due to columbic repulsion between the charges. Charges are then transferred to
the analytes (see Figure 5). The ions are typically adducts of H, ([M+H]+ ), adducts of salt ions such as
M+Na+, adducts of counter ions of the modifier e.g. M+NH4+ and M+CH3COO- . These ions don’t undergo
significant fragmentations. Therefore, the mass spectrum obtained with ESI is generally clean and
simple. Protonated or deprotonated molecular ions are typically observed.
ESI needle
Sheath or
nebulizing gas
Analyte
ion
Analyte solution
Charged
aerosol
Figure 5: Schematic diagram of an electrospray ionization device and ion formation process.
Molecules such as proteins that have multiple sites through which they can be protonated or
deprotonated can be multiply charged. The significance of this is that a large molecule can be observed
at a lower m/z. One advantage of ESI over EI or CI is that it is readily interfaced with liquid-based
separation techniques such as HPLC and capillary electrophoresis.
Matrix Assisted Laser Desorption Ionization (MALDI)
an Des
d ol
pr va
ot tio
on n
ati
on
The MALDI process is split into two steps: sample preparation and ion formation. During sample
preparation, the analyte to be transformed into ions is mixed with solution of a substance that is
referred to as the ‘matrix’. The solvent is evaporated and the solid residue that is produced is placed
under vacuum in the mass spectrometer, where it is irradiated with pulses of photons from a laser
source (Figure 6).
De
so
rp
tio
n
n
tio er
dia as
Ra m L
fro
hv
Matrix
Neutral Analyte
Figure 6: Schematic diagram of a Matrix assisted laser desorption ionization (MALDI) device and ion
formation process.
Energy from the photons causes a rapid heating of the crystals. This results in a localized ablation and
sublimation of the matrix crystals. Intact analytes are entrained in the plume that is formed. Ionization
can occur during this process via any of the following: proton transfer, ion–molecule reactions,
desorption of preformed ions.
MALDI is commonly used for studying non-volatile and thermally labile compounds such as proteins,
oligonucleotides, synthetic polymers and large inorganic compounds. Commonly used matrices are cyano-4-hydrocinnamic acid for peptides; 3,5-dimethyoxy-4-hydroxycinnamic acid for proteins and
polymers; 2,5-dihydroxybenzoic acid for peptides, proteins, lipids, and nucleic acids. 3 – hydroxypicolinic
acid is used for nucleic acid and DNA analysis. Laser sources that have been used include: nitrogen
(337nm), Nd:YAG (355 and 266nm) Er:YAG (2.94 m) and CO2 (10.6 m). Some advantages of this
method include: simple sample preparation and tolerance to contamination from salts, buffers and
detergents commonly used in sample preparation for biochemical analysis.
Atmospheric Pressure Chemical Ionization (APCI)
Atmospheric pressure chemical ionization (APCI) as the name indicates belongs to the group of ion
sources that are operated under ambient atmospheric pressures. The principle of operation of APCI is
similar to that of chemical ionization (CI) with the major difference that CI is operated under vacuum.
APCI is comprised of a heated nebulizing probe, a corona discharge electrode (typically a needle) and a
system of ion extraction lenses to transmit ions into a mass analyzer (see figure 1).
Figure 1: Schematic diagram of a typical atmospheric pressure chemical ionization (APCI) source
In operation, the analyte solution (typically delivered with a syringe or Liquid chromatograph) is directed
through a capillary tube (made of stainless steel or fused silica with ~120m internal diameter) at about
0.2-2ml/min into the APCI probe. A nebulizing gas at about 80psi is used to convert the solution into fine
droplets. A heated (100-500oC) coaxial sheath gas flow helps to evaporate and convert the droplets into
a stream of gaseous analyte and solvent molecules which are directed to the ionization region. The
ionization region contains a discharge electrode that is held at a high potential (2 to 3 kV) with respect
to the ion extraction lens.
Assuming nitrogen is utilized as the nebulizer and sheath gas, ions such as the N2+., N4+ , O2+. and NO+ are
formed in the corona discharge, These then interact with solvent molecules (e.g. water vapor from the
atmosphere or sample) in a cascade of reactions that culminates in the production of secondary ions
(e.g. water or solvent cluster ions). Reaction between the solvent ions and analyte molecules leads to
the formation of analyte ion. For example:
H3O  H 2O n  M 
 M   nH 2O
Application
This ion sources is typically used in LC-MS for less polar (e.g. PAH’, PCB, Fatty acids, Phthalates,
triglycerides), thermally stable compounds. When compared to electrospray (ESI), APCI is more tolerant
to contaminants that cause ion suppression. This makes it more useful for analysis of biological samples
that contain high salt concentrations.