Fundamental LC-MS Orbitrap Mass Analyzers PDF
Fundamental LC-MS Orbitrap Mass Analyzers PDF
Fundamental LC-MS
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i manual.
Aims and Objectives
Aims
Objectives
Explain the advantages and disadvantages of using the orbitrap mass analyser
List the main components of the orbitrap mass analyser
Explain how to perform the coupling between an orbitrap mass analyser and a
continuous ion source
Understand the principles of image current detection
Differentiate the different operative modes (FT and MSI) common to orbitrap mass
analysers and when to use each one of them
Recognise the importance of Fourier Transformation (FT) in signal processing
Recognise linear traps as very efficient ways of ion storage
Content
Introduction 3
Overview 4
Analyzer Anatomy 5
Equations of Motion 6
Continuous Ion Sources 7
Quadrupole Mass Analyzer 9
Linear Quadrupole Ion Traps 10
Curved Multipoles 11
Curved Linear Traps 12
Image Current Detection 14
Ion Injection 15
Fourier Transform (FT) Mode 17
Fourier Transform 18
Mass Selective Instability (MSI) Mode 19
Multiply Charged Ions 20
Tune and Calibration 20
High Molecular Weight Application 22
Low Molecular Weight Application 24
Comparison with Other Analysers 25
References 26
Ion trapping techniques are important tools in mass spectrometry. However, traditional ion
trap mass analysers have disadvantages in either performance (insufficient mass
accuracy, limited linear range, reduced charge capacity, etc.) or high complexity and cost.
The orbitrap,[1,2,3] a new type of mass analyser, has drawn attention due to its analytical
performance in terms of resolution, mass accuracy, space charge capacity and linear
dynamic range, relatively small size and cost.
Invented by Makarov, the orbitrap mass analyzer is based on the Kingdom trap which
uses a wire stretched along the axis of an outer cylinder enclosing the trapping volume.
Orbitrap mass analysers operate using a pulsed technique and as such the task of
coupling to any external continuous ion source was initially regarded as a serious
problem.
The main objective of this module is to introduce the orbitrap as a new type of mass
analyser capable of performing dynamic trapping.
The working principle of the orbital mass analyser is based on the orbital trapping of ions.
Injected ions cycle around the central electrode and at the same time oscillate along the
horizontal axis.[1,2] The orbitrap mass analyser (illustrated next) consists of two specially
shaped central and outer electrodes.
The orbitrap is a modification of the ion trap developed by Kingdon;[4] which uses a wire
stretched along the axis of an outer cylinder enclosing the trapping volume. If a voltage is
applied between the wire and the cylinder, then ions are attracted to the wire. Ions with
enough tangential velocity will cycle around the wire.
Fourier Transform (FT) mode: Measuring coherent oscillations in the axial direction
(image current detection)
Mass Selective Instability (MSI) mode: Involving ion ejection and collection onto a
detector
Orbitrap mass analysers operate with good sensitivity, high mass resolving power (up to
150000), mass accuracies in the order of parts per million and mass range up to 2000
Da/e.[3]
The orbitrap mass analyser consists of an outer barrel like electrode and a central spindle
like electrode along the axial axis. Both electrodes are connected to independent voltage
supplies.[1,2]
The outer electrode is split into two parts: one for ion excitation and the other for
detection. The working principles of this electrode are explained at the end of this module.
The space between the internal and external electrodes forms the measurement chamber
which is linked to a vacuum pump system to provide high vacuum conditions
(approximately 10-8 torr or lower).
If good signal and high resolution are required, then ions of each mass must have a
coherent movement, this is achieved by injecting them in a very short bursts (or ‘packets’).
Ion introduction can be efficiently performed after modification of the electric field at the
injection port. This can be achieved by using a field compressor which is a small portion of
the outer electrode.
k 2 r2 k r
U (r , z ) z ( Rm ) 2 Ln C
2 2 2 Rm
Quadro-logarithmic: This field is the sum of a quadrupole field of the ion trap
A(Z 2 r 2 / 2) and a logarithmic field of a cylindrical capacitor
A(Z 2 r 2 / 2 B Ln[r ]) .
2r z k Rm2
2
r r (1)
t t
2
m 2 r
d 2
r 0 (2)
dt t
2Z z
kZ (3)
t 2
m
Where, k is field curvature, Rm is a characteristic radius, C is a constant, z is the charge
hold by an ion of mass m.[5,6] Under suitable boundary conditions equations one to three
can be solved; the main results are shown opposite, a detailed explanation can be found
elsewhere.[5]
Out of the three characteristic frequencies , r , and Z only the axial frequency ( Z )
is completely independent of the energy and position of ions; therefore, only this
frequency can be used for mass analysis.
The equation of motion along the axial Z direction (equation 3) describes a simple
harmonic oscillator with solution:
2EZ
Z Z 0 cos( Z t ) sin( Z t )
k
Where E Z is the characteristic kinetic energy of the particle in the axial direction; the axial
frequency of oscillation is given by:
z
Z k
m
i
Simple Harmonic Oscillator.
d 2x
2
2 x
dt
The solution of this equation is of the form:
Where A, B and are constants, x is the coordinate of displacement in the time domain
(t).
Although orbitrap mass analyzers operate in a pulsed fashion, they can be coupled to
continuous ion sources. Ion storage devices had made possible this coupling.
Prior to injection into the orbitrap, ions are transported from the source at high pressure to
the storage device (usually a linear ion trap) at low pressure. The first two quadrupoles
shown opposite (guide and transport) are used to bring the ions through several stages of
differential pumping.
A set of transfer lenses between the storage quadrupole and the entrance of the orbitrap
is also included. The objective of this set of lenses is to accelerate and focus the ion beam
into the entrance channel of the analyzer.[3]
In quadrople mass analysing devices, electric fields are used to separate ions according
to their mass-to-charge ratio (m/z) as they pass along the central axis of four parallel
equidistant rods (or poles). Ion separation is performed by using controlled voltages
applied to the mass analyser rods which impart an electrostatic field inside the analysing
device.
In quadrople mass analysing devices electric fields are used to separate ions according to
their mass-to-charge ratio (m/z) as they pass along the central axis of four parallel
equidistant rods (or poles) that have applied to them.
Depending upon the magnitude of fixed direct current (DC) and alternating radio
frequency (RF) voltages voltages it can be arranged that only ions of certain masses are
allowed to pass the whole length of the quadrupole. Passing out of the quadrupole and
into a detector, the other ions being deflected onto trajectories which cause them to collide
with the rods and pass out of the analysing device.
The principle of the quadrupole was described by Paul and Steinwedel at the University of
Bonn in 1953,[7] carrying on work on ion focussing that had been carried out in Athens in
1951 by the electrical engineer Christophilos.
Linear (or two dimensional) quadrupole ion traps have been used to collect and inject
pulses of ions coming from continuous sources.
A linear ion trap includes two pair of rods which collect ions by using radio frequencies.
Simple plate lenses at the ends of the quadruple provide the DC trapping field. A slot,
made in one of the rods, allows ions being radially ejected.[8]
The linear ion traps utilize only an electrostatic potential for confinement of the ion beam.
This device has two electrodes placed on either side of a linear space to form the
electrostatic potential for the confinement. The ion beam is reflected repeatedly between
the two electrodes.
Linear quadrupole ion traps have some advantages over traditional ion traps:
However, the performance of a linear quadrupole ion trap is highly dependent upon
mechanical errors of construction. If the rods of the trap are not completely parallel, then
ions at different positions will experience different field strength, which in turn will cause
different ejection times.
Using curved quadrupole rods, this type of analyzer works in a similar fashion to the linear
counterpart.
The purpose of this modification is to force the ion beam to traverse a curved path prior to
the detector or a subsequent mass analyzer; by doing this, the incidence of photons
(coming from the ion source) and any other potentially interfering particles that could
reach the detector is minimised. As expected, this reduction renders a substantial
improvement in the signal to noise ratio.[9]
In the representation below, only ions with the desired mass to charge ratio will reach the
detector (left hand side). Note how, if the collision cell was linear, then photons would be
able to reach the detector (right hand side).
The movement of ions within the curved quadrupole closely resemble the movement
within linear quadrupoles.
As with traditional multipole devices, different rod geometries are currently available,
having circular, hyperbolic or even square cross sectional areas.[10]
Curved linear traps function in the same way as their linear counterparts with the added
advantage that ions can be focussed in narrow areas to be ejected as compact bursts of
ions.[13,14] This is usually achieved by altering the trapping fields of the electrodes at the
front and rear of the instrument.[15]
The presence of a collision gas (or bath gas) will reduce the kinetic energy of the ions
within the trap.
In the animation ions are focussed into a narrow area of the trap and then ejected through
the slot provided (made in one of the electrodes); however, ions can also be axially
ejected.
Curved linear traps provide an efficient way to feed ions to the orbitrap and therefore, are
used in several modern instrument designs.
Trapped ions can be detected in situ by measuring the image current they produce. The
main advantage of this technique is the ability to re-measuring ion populations.[16]
The image current detection technique has been successfully implemented not only in
conventional ion traps but in high mass resolution analysers (FT-ICR and
orbitrap).[16,17,18,19]
Ions populating the analyser describe different trajectories (according to the analyser
itself). A coherent excitation (DC pulse) is imposed to the ions in such a way that ions of
the same mass to charge ratio move coherently. Following the DC excitation, the image
current is measured on the detector electrodes.
The trajectories described for the ions through the quadrupole are complex and cannot be
described in a simple way; however, after a coherent excitation is imposed (usually a
pulse variation in the electrostatic field between rods) in such a way that populations of
ions will perform coherent oscillations between two opposite rods. The movement of ions
between the rods will induce an electric current that can be measured. As expected, the
intensity of the current is proportional to the number of ions. The principle of image current
detection is further explained below.
Ion detection is followed by a fast Fourier Transform algorithm to convert the recorded
time domain signal into a mass/charge spectrum.
In order to achieve high resolution with the orbitrap, then ions of each mass to charge
ratio must have a coherent movement and this is achieved by injecting them in a very
short time (or in bursts). The curved linear ion trap is one of the most efficient ways of
injecting ions to the orbitrap.[1,2,3,5,15]
Slow injection
Unlike linear ion traps, the curved linear ion trap allows ions to be injected into the orbitrap
at a position offset from its equator and in fact, by doing this, ions will perform coherent
axial oscillations almost immediately after injection without the need for any additional
excitation; this type of ion injection is known as “fast injection”.[16,17]
Fast injection
When ions are injected at an equatorial position, then ion oscillation is achieved by
imposing an additional excitation; this type of ion injection is known as “slow injection”.[1]
In order to eliminate gas carryover from the trap (linear or curved), the ion beam is usually
deflected by a set of transfer ions.
Ions within the orbitrap have three different frequencies of oscillation: axial, radial and
rotational.[1]
Feeding bursts of ions in the orbitrap at a position different to its equator, these
packets of ions will start coherent axial oscillations without the need for any
additional excitation
If a voltage pulse is applied to one part of the outer electrode, then ions (which
already populate the analyser in a disc area) will accommodate at certain axial
position; when the pulse is over, ions will coherently oscillate with harmonic motion
One or both parts of the outer electrode are then used to detect trapped ions by
measuring their image current (which is generated as the ions axially oscillate back and
forward).
The Fourier Transform of the signal can be used to produce the required mass spectrum.
This mode of detection yields the highest mass resolution that the orbitrap can achieve.
The Fourier Transform mode measures coherent oscillations in the axial direction (image
current detection).
Ion movement within the orbitrap comprises rotations around the central electrode with
axial oscillations; however, only the axial oscillations are important for ion detection.
The Fourier Transform (FT) is a mathematical operation that transforms one function in
the time domain to a second function in the frequency domain. If a function is to be
intergrated then its Fourier Transform function (also integrable) can be found.[22,23]
The FT theory is based on the idea that any integrable function can be expressed as a
summation of sines and cosines of different frequencies.
In signal processing the domain of the original function is usually time; the domain of the
new function is usually the frequency domain. Working in the frequency domain offers
some advantages including:
Collect information in ways that sometimes facilitate signal analysis (for example
periodic noise can be easily identified and removed)
By using FT is easy to go backwards and forwards from the time to the frequency
domain
There are many different ways in which FFT algorithms are implemented; however,
programming skills are required and therefore, we will not discuss this topic any further.
If f(x) is a continuous integrable function of a real variable x, then its Fourier Transform is
defined by:
2 uix
F (u ) f ( x )e dx
Given F(u), the original function f(x) can be easily recovered by using the inverse Fourier
Transform, which is defined by:
2 uix
f ( x) F (u )e du
The previous expressions are used with mathematic functions; however, their use in
signal processing is limited and discrete expressions are used instead:
N 1
1 2 uix / N
F (u ) f ( x )e
N x 0
N 1
2 uix / N
f ( x) F (u )e
x 0
The second mode of mass detection available with orbitrap mass analysers involves
ejection of the ions and collection on a detector (as is used with conventional mass
analysers like quadrupole, time of flight, magnetic sector, etc.).
Although the principal analysis method of the orbitrap is the FT mode (allowing the highest
mass resolution the equipment can achieve), there are some instances in which the MSI
mode should be used, for example ions with certain mass to charge ratio can be stored for
MS/MS analysis, or high intensity signals from unwanted compounds can be ejected to
improve dynamic range.[1]
Application of the appropriate frequency will results in excitation of oscillations and finally
ion ejection from the measurement chamber. A convenient means of detection of the
ejected ions is collision with a conversion dynode in the outer electrode, which generates
secondary electrons which can be accelerated to a detector.
Parametric resonance: the voltage applied to the electrodes is varied sinusoidally with
time
Resonance excitation: If the sinusoidally oscillations are applied to half of the outer
electrode (excitation electrode).
Ions exiting the orbitrap collide with a dynode generating secondary electrons, these
electrons are then multiplied, collected and detected.
Whether “parametric resonance” or “resonance excitation” is the best MSI mode for high
resolution depends on the application in which it is to be used.
Due to their high resolving power, orbitrap mass analysers can handle the MS analysis of
heavy and multiply charged molecules (which is the case in many different areas such as
in proteomics). Although other analysers can be used, the orbitrap possess combined
advantages of performance and price not possessed by any of its counterparts.[25,26]
The tune and calibration parameters of modern instruments can be easily reset to their
original values. This of overriding importance when starting your system after a complete
shutdown.
Caffeine
MRFA peptide
Ultramark
Bradikinin 1-9
MRFA peptide
Ultramark
SDS
Sodium taurocholate
Proteomics, the large scale study of proteins, is one of the most active and demanding
research fronts of MS. Due to its high performance, the orbitrap mass analyser is well
suited for protein structure elucidation.
In the application opposite,[30] a pure immunoglobulin gamma sample was infused into
an orbitrap mass analyser and then its ESI(+)-MS spectrum was recorded.
m1 (M n1 H ) / n1
m2 (M n2 H ) / n2
If the charge state of both peaks (n1 and n2) differs only by the addition of a single proton:
n1 n2 1
Then:
m2 H
n1
m2 m1
M n1 (m1 H )
Where M is the molecular weight of the analyte and H is the molecular weight of
hydrogen.
The average molecular weight found with the orbitrap (147252.3 Da) is in good agreement
with the theoretical value of 147250 Da, with an error of only 0.00159%.
Lipidomics, the large scale study of pathways and networks of lipids in biological systems,
is a very important research topic in Mass Spectrometry. Due to its high resolving power,
the orbitrap mass analyser can be used to differentiate molecules with identical nominal
mass (isobaric molecules).
The interactive example shown (please refer to the online material), illustrates how
resolution can be used to differentiate isobaric molecules. Please bear in mind
that:[34,35,36,37]
The spectrum corresponds to a sample that contains only two different isobaric
analytes
Labels “A” and “B” correspond to anionic pseudomolecular ions coming from the
deprotonation of each analyte within the sample and are of the form [M-1]-
Labels “A+1” and “B+1” correspond to the isotopic form of each pseudomolecular
ion previously defined (mainly due to the presence of 13C on each molecule)
The table below reports typical figures of merit for selected mass analysers.[38,39,40]
Please bear in mind that the resolving power depends upon the mass to charge ratio and
scan speed at which the instrument is operating. It is also important to note that
sensitivity depends upon the ionisation efficiency.