Mass Analyzers
After the production of ions in ion sources, the next critical step in mass spectrometry is to separate
these gas phase ions according to their mass-to-charge ratio (m/z). Ions are extracted from the ion
source and sent to a device called the Mass Analyzer (Figure 1a). Gas phase ions in motion can be
characterized by their momentum, kinetic energy, velocity, and response to electric or magnetic field.
Mass analyzers make use of one or more of these properties to distinguish between ions. There are
many types of mass analyzers and they can be classified in a variety of ways. One classification (based on
their general principle of operation) sorts them into two groups:


Mass filters are devices in which only ions of interest make it through the mass analyzer to the
detector (Figure 1b). All other ions are neutralized. Conditions on the mass analyzer are then
reset so that other ions are guided to the detector.
Beam analyzers are devices in which the ions are separated according to their m/z such that
each ion travels through the mass analyzer and arrives at the detector at q different time or
different location on q focal plane (Figure 1c).
Principles of the three most common types – magnetic sector, quadrupole and time of flight - will be
discussed herein.
Figure 1a: Ions produced in the ion source (blue and red dots) are extracted (from cloud of neutral
compounds and ions) and accelerated by the ion optics into the mass analyzer.
Figure 1b: General principle of operation of a mass filter. With mass filters a mixture of ions that are
continuously extracted by the ion optics are introduced into the mass analyzer. Under a set of
conditions imposed on the mass analyzer, only one group of ions (with a unique m/z) makes it through
to the detector (the red ones in the diagram). Other ions are neutralized and removed from the mass
analyzer (the blue ions produced in the ion course in Figure 1a).
Figure 1c: General principle of operation of beam analyzers. In an ideal situation, all m/z ions
successfully make it through the mass analyzer, but they arrive at the detector at different times or at
different points in space (i.e. the ions are spatially resolved). In the diagram, the blue and red ions will
make it to the detector at different times.
1. Magnetic Sector Mass Analyzers
Magnet
Ion tion
c
tra ics
x
E pt
o
Ion
fli
gh
t
tub
e
De Ion
tec
tor
Ion ce
ur
So
Figure 2: Schematic diagram of a magnetic sector instrument.
These are first generation mass analyzers that date back to the days of J.J. Thompson
experiment on analysis of positive rays. As the name indicates, they are comprised of a magnet
that typically is in a semi-circular shape. An ion flight tube runs through the magnet (see Figure
2). The interaction of ions with the magnetic field can be modeled by the following expression:
m B 2 r 2e

z
2V
Where m is the mass of the ion (in kg), z is the number of charges on the ion, e is the electronic
charge (1.602 x 10-19C), r is the radius of the ion path through the flight tube, V is the
acceleration potential of the ions and B is the strength of the magnetic field (in Tesla, T).
From this expression, it can be predicted that at a given value of B and V, ions with smaller m/z
will travel in a path of smaller radius compared to an ions with a bigger m/z ratio. However, only
ions that travel in a path that is similar in radius to the flight tube can successfully make it
through to the detector. Other ions travel in a path that leads them to collide with the wall of
the flight tube. They become neutralized and are pumped out of the tube under the prevailing
low pressure (~10-6 Torr) condition. Varying the magnetic field while keeping the acceleration
potential (V) constant will vary which ions (of select m/z) successfully make it through the flight
tube to the detector. Monitoring the signal that is generated by the detector for each group of
ions and plotting that signal versus the m/z of each group results in the mass spectrum
2. Quadrupole Mass Analyzers
Figure 3: Schematic diagram of a quadrupole mass analyzer.
The quadruple mass analyzer is also called a mass filter (Figure 3). It consists of four rods
(conducting metals). Separation of gas phase ions is achieved by creating an electric field that
makes the ions oscillate within the space between the rods. At a particular set of conditions,
only one m/z ion has the correct oscillation to make it through the quadrupole to the ion
detector. Other ions oscillate with so much amplitude that they collide with one of the rods and
are neutralized and pumped out of the system. To accomplish the oscillation, a positive dc
voltage is applied to one pair of the rods and a negative dc potential is applied to the other pair.
Additionally, an alternating radiofrequency voltage is superimposed on the rods. At an instant of
time, the ions are attracted to one pair of the rods and repelled by the other pair.
Figure 4: Representation of the pair of rods on the y-z plane of a quadrupole mass analyzer.
Assuming that the ions are positively charged, when they oscillate in the y-z plane (that is they
are vibrating in the y direction while travelling in the z direction), they experience repulsion
from the positively charged rod (Figure 4). This repulsion focuses them onto the z-axis. This is
strongly the case during the positive cycle of the superimposed rf potential. However, during
the negative cycle of the rf potential, the ions are slightly defocused away from the z-axis.
Relatively high m/z ions are less affected by this defocussing. Relatively low m/z ions are more
affected and can oscillate high enough that they collide with the rods. Upon collision with the
rods, they are neutralized and are removed from the analyzer chamber (i.e. they are filtered
out). With a certain combination of dc (U) and ac (Vsin t) potentials, a group of ions with
similar m/z will successfully travel through the analyzer to the detector. When the dc-ac
conditions are changed, another group of ions of another m/z will successfully navigate their
way to the detector. Repeating this process such that a range of ions (i.e. a range of m/z) are
eventually guided to the detector sequentially is called scanning. Two dimensionless
parameters, a and q (shown below) define the conditions for successful oscillation.
au   ax  a y 
8 zeU
,
m 2 ro2
Re-arranging we get:
qu   qx  q y 
4 zeV
m 2 ro2
m
8eU
m
4eV


and
2 2
z au ro
z qu 2 ro2
Where
 ro is the inscribed radius (or ½ the distance between opposite pair of rods, in ‘m’)
  = 2f, and ‘f’ is the radio frequency
 m is the mass of a single ion in kg
 e is electronic charge (1.602 x 10-19C),
 U is the dc potential (in V)
 V is the rf potential (in V)
During scanning, U and V are varied linearly to keep their ratio constant ( a/q = 2U/V ). At a
particular combination of U and V, values of a and q are set and this determines which m/z ion
navigates successfully though to the detector.
3. Time-of-flight Mass Analyzer
In a time-of-flight (TOF) mass analyzer, ions from the ion source are directed into a region where
they are repelled and accelerated into a field-free flight tube. The repulsion and acceleration of
an ion depends on its m/z ratio. Therefore, ions in the flight tube travel at different speeds and
arrive at the detector at different times (Figure 5).
Figure 5: Schematic diagram of a time-of-flight mass analyzer.
The time of arrival of an ion is given by the expression:
t
 m
L
 L 
v
 2qV



Or
t

L
m
 L 
v
 2 zeV



Where t is the time, v is the velocity, and L is the distance (in m) between the extraction optics
and the detector. L can be approximated with the length of the flight tube. Note that ions with
smaller m/z will travel faster and reach the detector sooner.
A TOF mass analyzer is calibrated with compounds of known molecular weight and fragments so
that the time can be related to several m/z values.
A generally accepted calibration equation is:
m
 at 2  b
q
A TOF mass analyzer is an example of a beam analyzer because all the ions in a packet are
transmitted to the detector.
4. Ion Trap Mass Analyzers
Ion traps are mass analyzers that can perform dual roles of ion storage and mass analysis. A few
things to note about ion traps are that:
 The ions are typically stored for only a limited period of time,
 There is a limit to the amount of ions that can be stored in a given device otherwise
development of space charge may lead to resolution problems.
 Ion traps can also function as molecule-fragmentation and mass a selective device
There are several kinds of ion traps which can be broadly classified as indicated in Figure 1
below:
Figure 1: A Classification of ion trap devices. Note: LIT means linear ion trap. QIT means
Quadrupole ion trap
The 3D QIT will be discussed here as an example (representative) of ion traps. Threedimensional quadrupole ion traps (3D, QITs’) are commonly employed in the GC-MS systems
that are frequently found in undergraduate laboratories. These devices confer multiple stage
mass spectrometric (MSn) capability, small size and low cost nature to the bench-top GC-MS
systems.
Figure 2: Schematic diagram showing the electrodes of a quadrupole ion trap (QIT).
Three-dimensional QIT’s comprise of three electrodes: two end-caps and a ring electrode (see
Figure 2). Both end cap electrodes have orifices for ion injection and ejection. An ion source is
placed in front of the entrance end-cap electrode and a transducer is positioned behind the exit
end-cap electrode. Operation of the QIT can be broken into following steps: ion injection, ion
trapping, ion fragmentation (if necessary), and sequential ion ejection and detection (i.e. mass
analysis). Each of the steps is further described below:
Ion Injection
Electron and chemical ionization devices are used for generating ions from thermally stable and
volatile molecules, while electrospray ionization device is used to generate ions from polar and
non-volatile molecules. These externally generated ions are extracted with appropriate lenses
into the trap. The amount of ions injected/extracted into the trap is controlled to avoid space
charge which can subsequently disrupt mass resolution. Ions are injected into the trap in
batches. The ions are trapped, fragmented (if necessary), analyzed and detected before the next
batch of ions is introduced trapping chamber.
Ion Trapping
Since the kinetic energies of externally generated ions are typically too high to permit efficient
trapping, a bath gas (e.g. helium) is allowed into the chamber to cause their collisional cooling
(i.e. the reduction of their kinetic energy). This cooling also enables the confining of ions to (or
near) the center of the trapping chamber. This is important because ions that travel closer to the
electrodes are easily lost due to the steeper gradient of the electric field near the chamber. To
sustain the ions in stable trajectories within the chamber, a high ac voltage called the
‘fundamental RF’ is applied to the ring electrode while the end caps are kept grounded. This
makes each ion to oscillate axially while travelling in a circular trajectory which is similar to the
Lissajous shape. Frequency of oscillation of the ions under this condition is called the ‘secular
frequency’. Ions of same m/z have a unique secular frequency of oscillation.
Ion Fragmentation
To facilitate fragmentation of the trapped ions, a small auxiliary RF voltage is applied to the endcaps. When the frequency of this auxiliary voltage matches the secular frequency of an ion, the
amplitude of its axial oscillation is increased and it collides with the bath gas and fragments.
Such an ion is described as tickled and the voltage that is used in effecting the excitation is called
the ‘tickle voltage’. Magnitude of the tickle voltage (or auxiliary voltage) is about 100mV.
Ion Ejection/Mass Analysis
A few methods are utilized for ion ejection from the trap but only the resonance ejection
approach will be described here for simplicity. To initiate resonance ejection of ions with a
particular m/z, first the corresponding fundamental RF is set, and the amplitude (magnitude) of
the auxiliary RF is increased until its frequency matches the secular frequency of the desired ion
(i.e. m/z). The trajectory of these ions is destabilized, as their axial oscillation increases and they
escape through the orifice of the exit end cap to the detector. The fundamental and auxiliary rf
voltages are then changed the next ion is then ejected.
Advantages of ITMS
a. ITMS generally have high sensitivity. This is facilitated by their ion storage/accumulation
ability, coupled with the fact that ions that are not of interest can be rejected.
Combination of these two factors leads to high signal –to-noise ratio and consequently
high sensitivities.
b. ITMS can be used for Multistage mass spectrometry (MSn) studies in which
parent/precursor ion can be fragmented, and the fragment can be further fragmented
to obtain structural information of molecules.
c. QIT in particular can be coupled with ions sources that are operated at modest (e.g. CI)
to high pressures (ESI).
d. The small size of these mass analyzers enables the design of bench-top mass
spectrometers (e.g. GC-MS).
Disadvantages
a. ITMS are not generally good for quantitation
b. They have limited dynamic range
c. Collision energies are not well defined when operated in the collision induced
dissociation (fragmentation) mode, thereby leading to irreproducibility of ions.
d. There are too many parameters to control to obtain quality mass spectrum
Describing Performance of Mass Analyzers
Several important parameters describe the performances of a mass analyzer
The mass range is the highest m/z that can be analyzed on a particular mass analyzer.
Resolution is a measure of the mass analyzer’s ability to separate and distinguish ions of similar masses.
Mathematically, it is calculated using the expression:
R
m2
m
Where m2 is the larger of the two masses and m is their difference.
Mass Accuracy is defined as the error in measuring the mass in m/z of a particular ion divided by its
calculated exact mass.
 mass error 
6
Mass Accuracy  
 10 ppm
 exact mass 
Mass Error = Exact Mass – Measured mass
(Note: measured mass is the experimentally measured mass while Exact Mass is the calculated mass
based on the sum of exact masses of each atom in the molecule). Tables of exact masses of atoms
are commonly available (e.g. http://www.nist.gov/pml/data/comp.cfm )