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MSU Is An Nan-native Action/Ema! Opponunlty Initiation
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A Segmented-Ring Ion Trap
Storage SourcelReflectron/‘l'ime-Of-Flight
Mass Spectrometer

by

Qinchung Ji

A DISSERTATION

Submitted to
Michigan State University
in partial fulfillment of the requirements
for the degree of

DOCTOR OF PHILOSOPHY

Department of Chemistry

1996

Abstract
A segmented ring ion trap storage source (SRS)

lreflectronltime-of-flight mass spectrometer
by

Qinchung Ji

The mass spectral detection of chromatographic eluents has suffered from trade-
offs of the spectral generation rate, mass resolution, mass range, sensitivity and
sample utilization efficiency. A segmented-ring ion trap storage source with
electron impact ionization has been developed for use with time-of-flight mass
analysis to overcome these trade-offs and provide high spectral generation rate
and excellent sensitivity without loss of mass spectral (discriminating)
information. During the ionization period, an RF voltage is applied between the
ring and end cap electrodes. Most of the ions generated in the ion source
accumulate there throughout the ionization period. A pulsed extraction of the
ions stored in the ion source is accomplished by switching the trap electrodes
from the RF storage voltage to the DC voltages required to provide a linear DC
extraction field essential for the TOP analysis. The application of the pulsed
extraction field is synchronized with the phase of RF voltage applied during the
ion storage period.

A mathematical model of a reflectron which is able to temporally focus

isomass ions at the detector surface was established. A numerical solution and a

general procedure for constructing a broad range energy focusing reflectron was
developed.

A segmented ring ion trap storage source/reflectron/ time-of-flight mass
spectrometer was fabricated. A gas chromatograph was interfaced to the time-of-
flight mass spectrometer. Without component optimization, better than unit mass
resolution is achieved through m/z 500 without the need for collisional ion
cooling which is mandated for quadrupole ion trap mass analysis. With an
extraction rate of 1 kHz and a recording rate of 4 spectra/s, a linear working
curve is obtained between 36 pg and 18 ng of chlorobenzene delivered
chromatographically. The detection limit for chlorobenzene is 36 picogram with
signal to noise ratio of approximately 50:1. The system has demonstrated the
potential to achieve the sought-for goals of very high sample utilization efficiency

at high spectral generation rates.

© Qinchung Ji
1996

Acknowledgment

It was a challenge and opportunity for me to start a project to develop a mass
spectrometer for my Ph. D. dissertation research. With the guidance of Professor
Enke and Professor Holland, the assistance of the people in and outside of
Professor Enke’s research group, I am glad that I got through it.

I would like to thank my advisor, Professor Enke. It is he who brought the
opportunity for me to work with this project. His trust, encouragement, and
guidance have made significant improvement in my abilities of learning, creative
thinking, Independent and collaborative researching, scientific presentation.

I would like to thank Professor Holland, who is the co-investigator and
consultant on this project and second reader of my Ph. D. dissertation. The
meetings with Professor Enke and Professor Holland during this project were
always stimulating and productive.

I would like to thank Professor McGuffin and Professor Braselton. I
learned a lot from their classes and discussion with them.

I would like to thank Michael Davenport. His help on the design and
construction of the dynamic voltage and timing system was critical to the

success of this project. I benefited a lot from working with him on electronic

construction. I would like to thank Dr. George Yefchak and Hewlett Packard Inc.
for providing me a data acquisition board with a computer software.

I would like to thank Fei Liu and Gregor Overney, good friends of my
family, for their friendship. Gregor, with his advanced computer knowledge, has
given me a lot of help also.

Dave McLane and Mary Seeterlin gave me a lot of help in the early
stages of this project. I have enjoyed working with Eric Hemenway, Paul Vlasak,
Calin Znamirovski, Paul Miyares, Douglas Beussman, Tina Erickson, Terri
Constantopoulous and Michele Davenport.

I would like to thank the people in the machine shops and electronic
shops at both Michigan State University and the University of New Mexico.

I would like to thank my former advisors, Professor D. F. Hunt at the
University of Virginia; Professor Dengqui An and Professor Longsheng Sheng at
China Pharmaceutical University, Professor Deshu Guan and Professor Xinming
Li at Dalian Institute of Chemical Physics, Chinese Academy of Science. They
help me lay the basis for starting my graduate study at Michigan State University
and for working in this project.

I would like to thank my wife, Hua Tang and our son, Minchuan. When I
was excited about my progress, she shared that joy with me. When I was upset
or frustrated, She gave me encouragement and discussed ways to solve the

problem. I would like to thank my parents. they came from China to help me so I

vi

have more time stay in the lab in the evenings and during the weekends for the

final year of my graduate research.

vii

Table of Contents

Chapter 1 Introduction ....................................................................... 1
1.1 Background ................................................................................................... 1
1. 1. 1 Sample utilization efficiency ............................................................... 2
1. 1.2 Spectrum generation rate .................................................................... 3
1. 1.3 Mass spectral resolving power ........................................................... 4
1. 1.4 Direction of the improvement of mass spectrometry detection
for gas chromatography .............................................................................. 5
1.2 Time-of-flight mass spectrometer ............................................................... 6
1.2. 1 Introduction ........................................................................................... 6
1.2.2 Spectral generation rate and time array detection ............................ 7
1.2.3 Mass resolution of the time-of-flight mass spectrometer ................. 8
1.2.4 Sample utilization efficiency ............................................................. 17
1.3 lon trap Mass Spectrometer ....................................................................... 17
1.4 Quadrupole ion trapltime-of-flight mass spectrometer ........................... 20

1.5 Segmented ring ion trap storage source/reflectronltime-of-tlight
mass spectrometer ..................................................................................... 21

Chapter 2 Theoretical development and computer simulation of
the segmented-ring ion trap source for the time-of-flight mass
spectrometer ..................................................................................... 28

viii

2.1 Background ................................................................................................. 28

2. 1. 1 Quadrupole ion trap .......................................................................... 28
2. 1.2 Cylindrical ion trap ............................................................................. 33
2. 1.3 Segmented ring ion trap .................................................................... 35
2. 1.4 Computer simulation .......................................................................... 35

2.2 Theoretical development and computer simulation of the segmented
ring ion trap as an ion trap storage device ............................................... 37

2.2. 1 Computer simulation of the equipotential field of the ion traps ...38
2.2.2 Computer simulation of Ion trajectories ........................................... 38
2.2.3 Effect of initial phase angle of RF field on the ion motion ............. 41

2.2.4 Relationship between the ion kinetic energy and the RF phase....49

2.2.5 Stability diagram of the segmented ring ion trap ............................ 51
2.2.6 Effect of bath gas collisional cooling ............................................... 54
2.2. 7 Conclusion ......................................................................................... 55

2.3 Development and computer simulation of the segmented ring ion trap
as an ion source for time-of-flight mass spectrometry ............................ 58

2.3. 1 Computer simulation of ion extraction from the quadrupole ion
trap storage source for time-of-flight mass analysis .......................... 58

2.3.2 Computer simulation of ion extraction from the segmented ring
ion trap .................................................................................................... 65

2.3.3 Proposed energy focusing method for time-of-flight mass
spectrometer analysis from the ion trap storage source ................... 68

Chapter 3 Theoretical development and computer simulation of a
broad energy range focusing reflectron for a time-of-flight mass
spectrometer .................................................................................................. 72

3.1. Background ................................................................................................ 72

3.2. Mathematical considerations .................................................................... 75

3.2. 1. Temporal focusing of isomass ions that start at the same
position but have different kinetic energy ................................................ 75

3.2.2 Temporal focusing of isomass ions with the zero initial kinetic

energy, but different initial positions in the ion source .................... 82
3.3. Computer simulation and practical design consideration ................... 90
3.4. Conclusion ............................................................................................... 109

Chapter 4 Design and construction of a segmented-ring
ion trap storage source/reflectronltime-of-flight mass

spectrometer ................................................................................... 112
4.1 Background ............................................................................................... 1 12
4.2 Design and construction of the time-of-flight mass spectrometer ...... 113
4.2. 1. Instrument overview ....................................................................... 1 13
4.2.2 Vacuum system ................................................................................ 115
4.2.3 Sample introduction ......................................................................... 1 17
4.2.4 Field free flight region voltage ........................................................ 1 18
4.2.5 Segmented ring ion storage source with electron impact
ionization .............................................................................................. 1 18
4.2. 6 Einzel lens and deflection plate ...................................................... 124
4.2. 7 Broad energy range focusing reflectron ....................................... 127
4.2.8 Detector ............................................................................................. 131
4.2.9 Electronic con trol system for the time-of-flight mass
spectrometer ........................................................................................ 131
4.2. 10 Data acquisition of the time-of-flight mass spectrometer .......... 138

Chapter 5 Characterization of the segmented ring ion trap
time-of-flight mass spectrometer .................................................. 141

5.1 Introduction ............................................................................................... 141

5.2 Mass resolving power of the SRSITOF mass spectrometer ................ 141

5.2. 1 The effect of RF phase at the time of ion extraction on mass

resolution .............................................................................................. 143

5.2.2 The effect of the electron bias voltage on mass resolution ......... 147

5.3 Characterization of ion storage of the segmented ring ion trap .......... 150
5. 3. 1 Ion loss for the normal electron impact ion source for

the time-of—flight mass spectrometer ...................................................... 150

5.3.2 Storage mass range with the RF voltage ....................................... 150

5.3.3 Ion buildup and ion storage of the segmented ring ion source ..150

5.4 Interface between gas chromatograph and the SRSITOF mass

spectrometer .............................................................................................. 160
5.4. 1 Dynamic working curve and Detection limit ................................. 160
5.4.2 Advantage of less interference from ion/molecule reactions ...... 166

Chapter 6 Significance and potential advantages for SRSITOF
mass spectrometer as a detector for chromatography ............. 174

xi

List of Figures

Figure 1-1. Schematic of four typical initial ion spatial and kinetic energy
distributions and their effects on the ion temporal distributions. Arrows
show the velocity vectors of ions with the same m/z. (a) Ideal situation
with zero initial spatial and kinetic distribution in the ion source. (b)
Initial spatial distribution but zero kinetic energy. (c) Initial kinetic energy
distribution but zero spatial distribution. (d) Same kinetic energy in
opposite directions but zero initial spatial distribution ........................... 10

Figure 1-2. Representative schematic of the Space Focus Plane formed along
the flight path due to initial isomass ion spatial distribution. Arrows show
the velocity vectors. The position and thickness of the Space Focus
Plane is related to the fields of the source and acceleration regions....12

Figure 1-3. Computer simulated function of a reflectron in a time-of-flight mass
spectrometer. The isomass ions in different positions in the ion source
form a space focus plane in the field free region. This small temporal
distribution is imaged to the detector position. The groups of red dots
show the ion positions along the flight path in equal flight time
increments ............................................................................................. 15

Figure 2-1. Stability diagram for the three-dimensional quadrupole ion trap ...... 30

Figure 2-2. Representative diagram of the parabolic pseudopotential well D, and
0,. The respective secular frequencies of ion oscillation within the wells
are a), and m, ........................................................................................... 32

Figure 2-3. Equipotential contours of the segmented ring ion trap. The red lines
are equipotential lines starting 25 V in 25 V increments. The endplates
are 0 V and ring electrode is 300 V (a) and 350 V (b) ........................... 39

Figure 2-4. Equipotential contours of (a) Cylindrical ion trap. (b) Quadrupole ion
trap. The red lines are equipotential lines from 25 V to 275 V in 25 V

intervals. The endplates are 0 V and ring electrode is 300 V ................ 40
Figure 2-5. The relationship between the ion storage time and the ion position in
the r and 2 dimensions in the segmented ring ion trap .......................... 42

xii

Figure 2-6. The relationship between the ion storage time and the ion position in
the r and 2 dimensions in the cylindrical ion trap ................................... 43

Figure 2-7. The relationship between the ion storage time and the ion position in
the r and 2 dimensions in the quadrupole ion trap ................................. 44

Figure 2-8. Computer simulated ion trajectory of an ion of m/z 100 for an RF of
1.2 MHz and 300 V (zero to peak) in the segmented ring ion trap ........ 45

Figure 2-9. Computer simulated ion trajectory of an ion of m/z 2000 for an RF of
1.2 MHz and 300 V (zero to peak) in the segmented ring ion trap ........ 46

Figure 2-10. The ion position in the z dimension vs. the ion storage time for ions
generated at four different RF phase angles. The RF phases for black,
red, green, blue lines are 0, n/2, n, 31t/4 ................................................ 47

Figure 2-11. The ion position in the z dimension vs. the ion storage time for ions
generated at four different RF phase angles. The RF phases for black,
red, green, blue lines are 0, 1r/2, 1c, 31c/4 ................................................ 48

Figure 2-12. The relationship between the ion kinetic energy and the RF phase
for ions generated at four different initial phases. The black, red, green,
and blue represent initial rf phases of 0, n/2, 1r, 31t/4 degrees .............. 50

Figure 2-13. Stability diagram of the segmented ring ion trap constructed by
computer simulation. The x axis and y axis show the RF and DC values
of the voltage applied between the ring electrode and the end plates..52

Figure 2-14. Stability diagram of the segmented ring ion trap constructed by
computer simulation. The a2 and q2 values were calculated using the
same equation as that for the quadrupole ion trap ................................ 53

Figure 2-15. lon position in the r dimension vs. ion storage time. The green line
is for a mean free path factor of 4x10 mm or 4x10 mm, the black line is
for that of 40 mm .................................................................................... 56

Figure 2-16. Ion position in the z dimension vs. ion storage time. The green line
is for a mean free path factor of 4x10 mm or 4x10 mm, the black line is
for 40 mm ............................................................................................... 57

Figure 2-17. Equipotential contours of a quadrupole ion trap during ion
extraction. Electrodes are in black, the red lines are equipotential lines
from 50 V to 750 V in 100 V intervals. The green lines are trajectories of
the ions extracted from the ion trap under the indicated extraction
voltages ................................................................................................. 60

xiii

Figure 2-18. Equipotential contours of a quadrupole ion trap during ion
extraction. Electrodes are in black, the red lines are equipotential lines
from 50 V to 750 V in 100 V intervals. The green lines are trajectories of
the ions extracted from the ion trap under the indicated extraction
voltages ................................................................................................. 61

Figure 2-19. Equipotential contours of a quadrupole ion trap during ion
extraction. Electrodes are in black, the red lines are equipotential lines
from 50 V to 750 V in 100 V intervals. The green lines are trajectories of
the ions extracted from the ion trap under the indicated extraction
vokages ................................................................................................. 62

Figure 2-20. Trajectories of ions extracted from a quadrupole ion trap. The green
lines are the ion trajectories. The red dots are ion positions along the
flight path at 0.5 us intervals. The m/z 100 ions are initially placed in the
segmented ring ion trap source in an X pattern. The voltages applied to
the electrodes are indicated .................................................................. 63

Figure 2-21. Equipotential contours of the segmented ring ion trap during the
ion extraction. Electrodes are in black, the red lines are equipotential
lines from 50 V to 750 V in 100 V intervals ............................................ 66

Figure 2-22. Trajectories of ions extracted from the segmented ring ion trap. The
green lines are trajectories. The red dots are ion positions along the
flight path at 0.05 us intervals. The m/z 100 ions are initially placed in
the segmented ring ion trap source in an X pattern ............................... 67

Figure 3-1. Schematic of potential profile of a reflectron and field free region...76

Figure 3-2. A representative diagram of a numerically constructed reflectron
profile. lsomass ions with increasing kinetic energy are stopped at later
reflectron grid positions ......................................................................... 79

Figure 3-3. Representative diagram of the ion extraction and reflectron voltage
profiles for the numerical construction of a reflectron voltage profile to
focus isomass ions extracted from the ion extraction region. lsomass
ions obtain different kinetic energies in the field free region due to their
different initial positions in the ion extraction region .............................. 83

Figure 3-4. Computer simulation of the ion trajectories (green lines) of m/z 100
ions initially at different positions in the ion source. The groups of red
dots show the ion positions at 0.5 ps intervals along the flight path. The
voltage profile applied to the reflectron is shown in Figure 3-5 ............. 91

xiv

Figure 3-5. The voltage profile applied to the reflectron shown in Figure 3-4. The
lowest energy ions turn around at the second reflectron grid position..93

Figure 3-6 .The voltage profile applied to the reflectron shown in Figure 3-7. The
lowest energy ions turn around after the fourth reflectron electrode ..... 94

Figure 3-7. Computer simulation of the ion trajectories of m/z 100 ions initially at
different positions in the ion source. The groups of red dots show the
ion positions at 0.5 us flight time intervals along the flight path ............ 95

Figure 3-8. Computer simulation of the ion trajectories (green lines) of m/z 100
ions initially at different positions in the ion source. The groups of red
dots show the ion positions at 0.5 us along flight path .......................... 97

Figure 3-9. Equipotential contours of the reflectron in Figure 3-8. The deviation
of the voltage profile in the center of the reflectron from the voltage
profile applied to the reflectron electrodes creates a distortion of the
desired field and introduces an ion lensing effect ................................. 98

Figure 3-10. Voltage profile applied to the reflectrons shown in Figures 3-11, 3-
12, 3-13 ............................................................................................... 100

Figure 3-11. Computer simulation of ion trajectories (green Lines) of m/z 100
ions initially at different positions in the ion source. The groups of red
dots show the ion positions at 0.5 us intervals along the flight path....102

Figure 3-12. Computer simulation of ion trajectories (green Lines) of m/z 100
ions initially at different positions in the ion source. The groups of red
dots show the ion positions at 0.5 us intervals along the flight path....103

Figure 3-13. Computer simulation of ion trajectories (green Lines) of m/z 100
ions initially at different positions in the ion source. The groups of red
dots show the ion positions at 0.5 us intervals along the flight path....104

Figure 3-14. Equipotential contours (red lines) of the reflectron in which the
second reflectron electrode is covered with a grid (a) or not covered
with a grid (b) as shown in Figure 3-12 and Figure 3-13 respectively.
Electrodes are in black and equipotential lines are red ....................... 106

Figure 3-15. The voltage profiles applied to the reflectrons shown in Figures 3-
13, 3-16. The red line is obtained from calculation for perfect temporal
energy focusing. The black line represents the linear voltage profile
applied to the reflectron shown in Figure 3-16 .................................... 107

Figure 3-16. Computer simulation of ion trajectories (green Lines) of m/z 100
ions initially at different positions in the ion source. The groups of red
dots show the ion positions at 0.5 us intervals along the flight path....108

Figure 4-1. A block diagram of the reflectron time-of-flight instrument with
segmented-ring ion trap source ........................................................... 114

Figure 4-2. A detailed diagram of the vacuum system for the time-of-flight mass
spectrometer. 1. Rough pumps; 2. Filters; 3. Butterfly valves;
4. Thermocouple gauges; 5. Turbo Pumps; 6. ISO/CF adapter; 7.
Fourway cross source chamber; 8. Flight tube; 9. Flange for reflectron
mounting; 10. Flange for detector mounting; 11. Flange for source
mounting; 12. View port ....................................................................... 116

Figure 4-3. Detailed drawing of the source ring element (a) and a cross section
view of the segmented-ring ion trap storage source with acceleration
electrodes and filament for electron impact ionization (b) The thickness
of the electrode element in Figure 4-2(a) changes from 0.01, 0.02 to
0.03 inches as the color of the part changes from light to dark ........... 119

Figure 4-4. Equipotential contours of the ion source during the ion extraction
period. The voltages across the acceleration electrodes are -600 V, -
1200 V, -1800 V. The voltages applied to the exit end cap, two ring
electrode elements, and the rear end cap are 0 V, 200 V, 500 V, 700 V.
The voltages applied to the electron entry electrode, the filaments and
the electron shield electrodes are 0 V, -25 V, -50 V. The red lines are
contours from 50 to 650 V in 100 V increments ..................................... 121

Figure 4-5. Computer simulation of electron trajectories (green lines). The
voltage of two end caps is 0 V. The electron entry electrodes, the
electron shield electrode and the filaments are CV, -50 V and -25 V. The
voltage of the ring electrode is 0V (a),-300 V(b), 300 V (c) ................ 123

Figure 4-6. A detailed drawing of the Einzel lens ............................................. 125

Figure 4-7. A computer simulation the ion trajectories( green lines) through a
Einzel lens assembly( black ).The voltage applied to the lens electrodes
are 0 V. -1500 V, 0 V. The ions have a kinetic energy of 1800 eV. The
red lines are equipotential contours from -300 V to 1200 V in 300
Vincrements. The group of blue dots represent the ion positions at 0.1
us along the flight path ........................................................................ 126

Figure 4-8. Computer simulation of the two states of the deflection plate. During
the ionization period (a) the deflection plate was a more positive voltage
than the field free voltage as shown. The red lines represent the

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equipotential contours from -1200 V to -1800 V at 50 V increments. The
green lines are ion trajectories of ions with 1800 eV kinetic energy. They
are bent as they pass the deflection plate. During the ion extraction
period (b), all of the electrodes have the field free voltage. Ions pass
without bending ................................................................................... 128

Figure 4-9. A diagram of the cross section of the reflectron assembly. The
reflectron ring electrodes are stainless steel rings with a 4.5 inch outer
diameter, a 3 inch inside diameter, and a 0.03 inch thickness. The linear
field between the first and second grid is generated by connecting the
reflectron ring electrode with 3 M9 resistors. Twenty-two electric
feedthroughs are used to provide individual tunable voltages to the
reflectron electrodes ............................................................................ 130

Figure 4-10. A diagram of the “Chevron assembly" detector design (a) and the
detail drawing of the ring electrode (b). Microchannel plates are in red
color. The anode is floating and the ion entry electrode is set at the
same voltages as field free region. The voltage across the three bias
voltage electrodes is around 1700-2000 V according to the gain
required ............................................................................................... 132

Figure 4-11. Schematic of DC voltage supplies for the ion source, Einzel lens,
and the detector ................................................................................... 133

Figure 4-12. Schematic of the voltage supply for the reflectron electrodes ...... 135

Figure 4-13. Schematic of the timing control and dynamic voltage supply to the
source electrodes ................................................................................ 136

Figure 5-1. The mass spectrum of PFTBA obtained at v, =800 volts (peak to
peak). f": 1.2 MHz. The insets illustrate the resolution at three points
along the mass axis at m/z 131, 219, and 502 .................................... 142

Figure 5-2. Synchronization of the extraction pulse with RF phase at RF phases
of (a)270° , (b)0° , (0)900 and (d)180° ................................................. 145

Figure 5-3. The effect of filament bias voltage on the peak height (a) and the
peak area (b) of the major ions of chlorobenzene ............................................. 149

Figure 5-4. The peak area of m/z 43 ion of acetone vs. the delay time between
cessation of ionization and ion extraction ............................................ 151

Figure 5-5. Mass spectra of PFTBA taken with various RF voltages on the ion

trap. As the RF voltage is increased, increases in both low mass and
high mass cutoff occur ......................................................................... 153

xvii

Figure 5-6. The effect of DC offset on the ion storage mass range .................. 155

Figure 5-7. The abundance of the major ions of chlorobenzene as a function of
(a) continuous ionization time and (b) extraction delays after an
ionization time of 142 us and (c) 342 us. The RF applied is 600 volts
(peak to peak) and 1.2 MHz ............................................................... 157

Figure 5-8. Ion build-up curves of major ions of PFTBA at oven temperatures of
(a) 25 °c, (b) 34 °c, and (c) 44 °c .................................................... 159

Figure 5-9. A working curve for chlorobenzene illustrating a linearity of response
over nearly three orders of magnitude ................................................. 162

Figure 5-10. A reconstructed ion chromatogram (RIC) for m/z = 112 for 36 pg of
chlorobenzene detected. Due to the noise near the detection limit, a
peak finding technique (threshold = 20) was used .............................. 163

Figure 5-11. Mass spectrum of spectrum no. 19 from the RIC of Figure 10 with
background subtraction. This spectrum is obtained by summing 256
transients ............................................................................................. 164

Figure 5-12. A reconstructed ion chromatogram (RIC) for m/z = 112 for 36 pg of
chlorobenzene detected. A ion deflection electrode was used to deflect
background ions during the ionization period ...................................... 167

Figure 5-13. Mass spectrum of spectrum no. 34 from the RIC of Figure 12 with
background subtraction. This spectrum is obtained by summing 256
transients. Each MCP plate of detector has 980 V across and most
background ions are deflected during the ionization period ................ 168

Figure 5-14. The intensity of major ions of benzophenone vs. amount of sample
introduced (a) and the peak area ratio of [M+1]" /[M]* of bezophenone
vs. amount of sample introduced (b) ................................................... 170

Figure 5-15 Spectra of Benzophenone obtained from different instruments.

(a) MSDB data base. (b), (c) SRS/TOF mass spectrometer. (d) ITMS
with external electron impact ionization .............................................. 171

xviii

List of Tables

TABLE 5-1. Effects of the timing of the extraction pulse in relation to the RF
phase ...................................................................................................... 146

xix

CHAPTER 1. INTRODUCTION

1.1 Background

In the 1980s, a group of scientists at Michigan State University realized that the
advantage of combining gas chromatography with mass spectrometry was
limited by the capabilities of the mass spectrometer‘. Developments in
chromatographic techniques had created a need for dramatic improvements in
the spectral generation rate, sample utilization efficiency and mass range for
mass spectrometric detectors.

For gas chromatography/mass spectrometry analysis, components of a
mixture separated by a chromatograph enter the ion source of a mass
spectrometer continuously. Typically, samples are ionized by electron impact
ionization. Ions generated in the ion source are mass analyzed in either of two
ways. In the first type of mass spectrometric analysis, all of ions in the ion source
are transferred continuously to the mass analyzer and ions are analyzed
exclusively and sequentially based on their m/z value. The m/z value of the ion
is recognized by scanning a transmission window, which allows only ions of
certain range of m/z values to pass through to the detector. Electronic properties
(such as magnetic strength, DC offset and RF amplitude) that are applied to the
mass spectrometer are varied to allow scanning of the mass window across the
mass range of interest. The commonly used mass spectrometers of this type are

the magnetic sector mass spectrometer and the quadrupole filter mass

spectrometer. In the second type of mass spectrometric analysis, ions are mass
’ analyzed in separate batches; all the ions with different m/z values in each
individual batch are analyzed simultaneous or within a short period. The
commonly used mass spectrometers of this type employ Fourier Transform mass
spectrometry (Fl’ MS), Time-of-Flight mass spectrometry (TOFMS) and Ion Trap
Mass Spectrometry (ITMS). The batch mass analysis of ion packets with
different m/z values is called time array detection (for TOFMS), frequency array

detection (for FT MS), and sequential destabilization scanning (for ITMS).

1. 1. 1 Sample utlllzatlon efflclency

Sample utilization efficiency is defined as the ratio of the number of ions
detected to the number of sample molecules introduced into the ion source. It
depends on the sample ionization efficiency, the ion transfer efficiency, and the
sample utilization duty cycle. This duty cycle can be defined as the fraction of
the time of each analysis cycle during which detectable ions are being generated
and measured.

For the scanning type of mass spectrometric analysis, the sample
utilization efficiency suffers from a low duty cycle. For example, for a scan range
of 500 mass units and a unit resolution mass window, individual m/z ions can at
most only be detected over one five hundredth of the scan period; During the
remaining 99.8% of the scan, this particular rn/z value ion is lost. The scanning

duty cycle is 0.2%.

spectrometer. In the second type of mass spectrometric analysis, ions are mass
analyzed in separate batches; all the ions with different m/z values in each
individual batch are analyzed simultaneous or within a short period. The
commonly used mass spectrometers of this type employ Fourier Transform mass
spectrometry (FT MS), Time-of—Flight mass spectrometry (TOFMS) and Ion Trap
Mass Spectrometry (ITMS). The batch mass analysis of ion packets with
different m/z values is called time array detection (for TOFMS), frequency array

detech’on (for FTMS), and sequential destabilization scanning (for ITMS).

1. 1. 1 Sample utlllzatlon efficiency

Sample utilization efficiency is defined as the ratio of the number of ions
detected to the number of sample molecules introduced into the ion source. It
depends on the sample ionization efficiency, the ion transfer efficiency, and the
sample utilization duty cycle. This duty cycle can be defined as the fraction of
the time of each analysis cycle during which detectable ions are being generated
and measured.

For the scanning type of mass spectrometric analysis, the sample
utilization efficiency suffers from a low duty cycle. For example, for a scan range
of 500 mass units and a unit resolution mass window, individual m/z ions can at
most only be detected over one five hundredth of the scan period; During the
remaining 99.8% of the scan, this particular m/z value ion is lost. The scanning

duty cycle is 0.2%.

In TOF and FTMS mass spectrometric analysis, the duty cycle depends
on the fraction of the batch mass analysis cycle during which detectable ions are
generated and maintained in the ion source. The mass analysis time for TOF-
MS is about 100 us. While ions can be generated throughout this period, thermal
motion of the ions created will carry most of them out of the source before they
are analyzed. Unless some ion storage mechanism is invoked, only the ions
created in the few microseconds prior to extraction will be analyzed. The
sampling duty cycle is 1-2%.

For ion trap mass spectrometry, the ions are generated and stored in the
ion source during the ionization portion of the analysis cycle. The duty cycle is .
thus dependent upon the ratio of the ionization/storage period to the total mass
analysis cycle. This is always less than unity due to the ion cooling and mass
analysis portions of cycle. 'In addition, at higher sample concentrations, ion
production is automatically curtailed to avoid saturation of the ion trap capacity

(limited to ~106 ions).

1. 1.2 Spectrum generation rate

The spectral generation rate for all types of mass spectrometers is limited by
some fundamental properties‘. In scanning mass spectrometers, higher spectral
generation rates are achieved by sacrifices in mass range, resolution or
sensitivity. Narrowing the mass range, such as in the selected ion monitoring
(SIM) technique, shortens the spectral data acquisition cycle, but limits the

amount of the spectral information obtained during each cycle. Scanning filter

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mass spectrometers and ion trap mass spectrometers all involve some finite time
to scan over the desired mass range. The spectrum generation rate is therefore
limited to the mass range divided by the maximum scan rate. The mass analysis
period for TOF mass spectrometers is set by the flight time of the ion with the
highest m/z value to be detected. This is generally less than 200 as, allowing a
maximum spectral generation rate in excess of 5000 Hz for the entire mass
range. Due to the physical nature of this technique, a transient waveform strikes
the detector in an increasing m/z sequence after every source extraction. This
waveform or transient, contains information for a complete mass spectrum,
however, it is usually not converted and stored as an individual spectrum at this

rate.

1. 1.3 Mass spectral resolving power

For scanning mass spectrometry, the resolution can be improved by decreasing
the window size of mass analysis. This slows the scanning rate. For magnetic
sector mass spectrometry and quadrupole filter mass spectrometry, a narrower
mass window will result in a smaller fraction of the ions reaching the detector
over the whole mass range. For ITMS, the resolution is also improved by using a
slower scanning rate. Scanning the ITMS more slowly results in a lower duty
cycle, therefore a lower sample utilization efficiency.
For TOF and FI'MS mass spectrometry, the resolution is not related to the
sample utilization efficiency. FTMS can provide extremely high mass resolution

but it requires an ultra high vacuum that is not readily compatible with sample

1.1

cm

introduction through a gas chromatograph. The very high mass resolution is
obtained by summing a large quantity of frequency domain transientsz. This
reduces the spectrum generation rate significantly. The resolution of a time-of-
flight mass analyzer is related to the design of the ion optics and the electronics

incorporated in the instrument.

1. 1.4 Direction of the improvement of mass spectrometry detection for gas

chromatography

A time-of-flight mass spectrometer can produce several thousands of transients
each second, this gives a fundamental measurement base for fast GC/MS
detection. The sample utilization efficiency of TOFMS could be improved by
implementing some kind of ion storage between ion extractions for TOF
analysis. The mass resolution could be improved by innovative ion optical and
electronic control design. The improvement of the mass resolution and sample
utilization efficiency of the time-of-flight mass spectrometer, while keeping its
fast spectrum generation rate, has been a research direction in Professor Enke’s
group and the MSU/NIH Mass Spectrometer Facility for many years. These
goals are essential to achieve the full capability of mass spectrometric detection
subsequent to chromatographic separation. The goals of fast spectral generation
rate and high sample utilization also require fast detector electronics and
continuous recording of the individual extraction transients generated at their

maximum rate.

1 .2 'I'Ime—of-fllght mass spectrometer

1.2. 1 introduction

The principles of mass analysis in TOF mass spectrometry can briefly be
described as follows. Ions are either generated in the ion source, mainly by
electron impact ionization, or introduced into the source region from an external
ionization source such as electrospray, or API (atmospheric pressure ionization).
The ions in the ion source are then extracted by the application of a short high
voltage pulse across the ion source volume. Ions with different m/z values gain
equal amounts of kinetic energy. These ions are directed through a field free
region where they will be separated on the basis of their differing velocities. Ions
with lower m/z values have higher velocities and will reach the detector earlier.
Ions with higher m/z values have lower velocities and will reach the detector
later. The arrival times of the isomass ion packets reaching the detector and the
detector response to the consecutive isomass packets are recorded as a time
domain transient. Each time domain transient can be converted into a mass
spectrum.

Time-of-flight mass spectrometry was first introduced by Cameron and
Eggers3 in 1948. In 1955, Wiley and McLaren developed this technique and
demonstrated its practical usefulness‘. Time-of-flight mass spectrometry was
also the first mass spectrometry technique to be interfaced with gas
chromatography“. However, TOFMS was soon eclipsed by magnetic sector

mass spectrometry and then scanning quadrupole mass spectrometry for

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chromatographic detection due to the higher resolution and easier interface of
the scanning instruments. Recently, time-of-flight mass spectrometry has gained
renewed attention due to its simplicity, fast spectral generation rate and
unlimited mass range“. The mass resolution has been improved significantly
because of the theoretical and practical developments in ion optics and

7 ,8 ,9 ,15

electronic control systems (such as the ion reflectron , high voltage

10,18

extraction pulse, and dynamic field ion focusing ). The spectral output has

been improved significantly because of the developments of the transient

recorder and computer control systems11 "2'13.

1.2.2 Spectral generation rate and time array detection

For time-of-flight mass spectrometry, the spectral repetition rate is limited by the
flight time of the heaviest (slowest) ion to reach the detector after being
extracted. For a 1 meter flight tube reflectron/time-of-flight mass spectrometer
and an ion kinetic energy of 1800 eV, an ion with an m/z value of 800 daltons
requires a flight time of less than 100 us. For this) upper mass limit, the time-of-
flight mass spectrometer is able to generate more than 10,000 transients each
second. If an analog oscilloscope is used, transients are displayed on the screen
repeatedly. Since the detection of the complete transient is essentially the
acquisition of an entire array of time domain data, the term time-array detection
is used for this detection scheme. However, it is not practical to encode and
store each transient as an individual mass spectrum at the maximum transient

generation rate. Fortunately, even for very fast chromatography, it is not

necessary to generate 10,000 individual mass spectra each second.

Scientists at the MSU/NIH Mass Spectrometry Facility have invented a
time-array detector called the integrated transient recorder which can acquire the
information from 10,000 transients each second”. Several consecutive
transients are summed together to give an individual mass spectrum in the time
domain. If 10,000 transients are generated by the time-of-flight mass
spectrometer each second and 100 successive transients are integrated into one
mass spectrum, this integration will reduce the mass spectral generation rate
from 10,000 spectra/s to 100 spectra/s which is an excellent mass spectral
generation rate for capillary GC/MS. Also the integration of the 100 individual
transients will improve the signal-to-noise ratio of each spectrum by a factor of
1 0 which is the square root of the number of summed transients. Because the
ion residence time in the ion source is about 2 #8, due to thermal motion of the
ions, the 10,000 Hz extraction rate provides a sample utilization duty cycle of

2%, If the extraction rate were slower, the duty cycle would be even less.

1.2.3 Mass resolution of the time-of-flight mass spectrometer

1.2.3.1 Initial spatial and kinetic distribution

The mass resolving power can be calculated as the temporal distribution of a
particular isomass ion packet at the detector position divided by its total flight
time. Although the ion optical path and ion extraction electronics have major

effects on the mass resolving power, they can be optimized, often leaving the

initial kinetic energy and spatial distribution of the ions in the ion source as the
two major factors which are limiting the mass resolution. The effects of these
factors on the exit times and velocities for isomass ions are shown in Figure 1-1.
The ideal situation, one that has zero initial spatial and velocity distribution, is
shown in Figure 1-1(a). lsomass ions leave the ion source at the same moment
with the same velocity. The effect of spatial distribution is shown in Figure 1-
1(b). lsomass ions located at different source positions experience different
extraction voltages. They leave the ion source with different velocities and at
different times. The effect of the kinetic energy distribution is shown in Figure 1-
1(c). The ions leave the ion source with different velocities and times because of
their different initial velocities. An extreme case of Figure 1-1(c) is shown in
Figure 1-1(d). Two ions have the same initial velocity but in opposite directions.
These two ions leave the ion source with the same velocity but at different times.
This time difference is called the tum-around time. The turn-around time causes
a more significant detrimental effect to the isomass temporal distribution at the
detector than the energy distributions in the same direction as shown in Figure
1-1(c), therefore, the turn-around effect has received greater attention as

discussed in a later section.

0

1.2.3.2 Space focus plane and two stage extraction

The initial spatial distribution of the isomass ions in the ion source as shown in
Figure 1-1(a) contributes significantly to the ion velocity difference of these

isomass ions. If not corrected, this velocity difference will cause significant

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distributions and their effects on the ion temporal distributions. Arrows show the
velocity vectors of ions with the same m/z. (a) Ideal situation with zero initial
spatial and kinetic distribution in the ion source. (b) Initial spatial distribution but
zero kinetic energy. (c) Initial kinetic energy distribution but zero spatial
distribution. (d) Same kinetic energy in opposite directions but zero initial spatial
distribution.

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temporal distribution at the detector position. In 1955, Wiley and McLaren
defined the concept of the Space Focus Plane and introduced a way in which it
could be moved to the surface of the detector, which significantly improved the
resolution of time-of-flight mass spectrometry as shown in Figure 1-2. The
isomass ions in the ion source are extracted from the ion source by applying a
linear voltage across the ion source. The ions near the back of the ion source
are extracted from a higher potential position. They spend more time in the ion
source but gain more kinetic energy and exit with a higher ion velocity. The ions
near the front side of the ion source are extracted from a lower potential position.
They spend less time in the ion source and leave the ion source earlier but gain
less kinetic energy and therefore have a lower ion velocity. At some position
along the field-free flight path, the faster ions from the rear of the source will
catch up to the slower ions starting from the front. Thus isomass ions originating
from different positions in the ion source will form a minimal temporal distribution
at a particular position along the flight path. This position is called the space
focus plane (or space focus position) and it is independent of the rn/z value of
the ion. Wiley and McLaren added a second acceleration region to the ion
source extraction field, so that the space focus plane could be set at the end of
the flight path (the detector position) by adjusting the ratio of the extraction field
and acceleration field. In this way, arrival time dispersion due to the initial spatial
distribution is reduced and an improved mass resolution is obtained. The

resolution of the mass spectrum recorded at the space focus plane is dependent

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on the ratio of the extraction voltage across the ion source to the acceleration
voltage. As this ratio is increased, the resolution is decreased. A higher

acceleration voltage results in better resolution‘.

1.2.3.3 Time lag focusing

Wiley and McLaren also developed a technique termed time lag focusing which
is able to minimize the effect of the initial energy distribution as well as turn-
around time (as shown in Figure 1-1(d)). Assume two isomass ions are
generated at the same position in the ion source but have equal initial velocities
in opposite directions. A time lag is applied between ion generation and ion
extraction. During the time lag period, the ion moving toward the front extraction
plate will move to a position where a lower extraction field will be experienced at
the time that the ion extraction pulsed is applied. The ion moving backward will
move to a new position where a higher extraction voltage will be experienced
when the ion extraction pulse is applied. After the ion extraction pulse is applied,
the ion turn around time of the ion moving backwards will be compensated by
the higher velocity gained from the higher extraction voltage it experiences. The
initial forward velocity of the forward-moving ion will be compensated by the
lower extraction voltage. At some position along the flight path, the isomass ions
will converge. The optimum lag period between ionization and extraction is
dependent on the initial velocity of the ions and the W2 value of the ions. Only a
limited fraction of the entire mass spectrum is focused for each value of the lag

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1.2.3.4 Reflectron

In 1973 Mamyrin introduced the electrostatic reflectron into time-of-flight mass
spectrometry“. A reflectron is an assembly of electrodes located at the other
end of the flight tube which acts as an ion mirror. The operation of a reflectron in
a time-of-flight mass spectrometer is shown in Figure 1-3. The groups of red
dots represent ion positions along the flight path in equal flight time increments.
The green lines represent ion trajectories. The black lines represent the
electrodes. Ions are initially placed in the ion source at different positions. The
electric field of the reflectron decelerates incoming ions and changes their flight
direction back into the flight tube. A reflectron is able to image isomass ion
packets at the detector position while the total flight length and time are
increased.

As discussed in more detail in Chapter Three, since a reflectron can
correct only for energetic differences, it can theoretically give perfect correction
of ion broadening due to the original spatial distribution (similar to the situation
at the ion source shown in Figure 1-1(b)) or initial kinetic energy distribution
(similar to the situation at space focus position). But a reflectron is not able to
correct both initial energy and space distribution simultaneously and it can do

nothing to correct the turn-around time.16

1.2.3.5 Dynamic focusing

Dynamic focusing is a technique which modifies the ion behavior after ions are

extracted from an ion source. It could involve a change in some aspect of

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distance, time, velocity or acceleration. Krnsel and Johnston introduced a
dynamic focusing technique termed post source pulse focusing". This method
Involves the application of a focusing voltage pulse to a short field region located
after the source and acceleration regions. The pulse is timed so that it occurs
after the ions of interest have entered this region. All the ions that are entirely
within the dynamic field region will show a substantial improvement in resolution.
All the ions which have already exited the acceleration region will not be
affected.

Yefcheck, Enke and Holland developed a dynamic focusing technique
termed dynamic field focusing". Two field-free regions exist in the ion flight
path. Ions are extracted from a single field source and enter the first field-free
region. The space focus plane is located in the first-field free region. The
dynamic field region is located between the field-free regions. Ions will be
accelerated as they leave the first field-free region and enter the second field-
free region. The acceleration is time-dependent because the voltage of the
dynamic field region varies with time. The mathematical derivation and computer
simulation indicated that concurrent space and energy focusing over a wide
mass range is possible and unit resolving power can be achieved up to at least
2000 amu with typical gaseous source conditions. In practical terms, the
achievement of the derived wave-shape for dynamic field operation would be
challenging. This approach has never been implemented in an operational mass

spectrometer.

17

1.2.4 Sample utilization efficiency

In 1989, Wollnik, Grix et, al., introduced an ion source design which used
electron impact ionization. The intention of Grix’s source design was to generate
a potential well by using two more negative voltage electrodes inside the
ionization region”. However, experiments showed that the negative voltage
applied to these electrodes did not generate a potential well as expected”). The
potential well that was formed was generated by the electron beam which is
focused into the ion source by an appropriate voltage setting to the source
electrodes”. Different variations on the Grix ion source design were
experimented with at the MSU/NIH Mass Spectrometry Facility to enhance the
potential well formed by the electron beam. Because the electron beam shape is
affected by very small changes in electrode configuration, repeatable
experimental results were difficult to obtain.

Another idea that existed in Professor Enke’s group for improving the
sample utilization efficiency of the time-of-flight mass spectrometer was to
improve the duty cycle by using a RF ion trap to continuously accumulate ions
generated between extractions. This concept initiated the research project that is

the basis of this dissertation.

1.3 lon trap mass spectrometer

The quadrupole ion trap is an ion storage device which was first disclosed by
Paul and Steinwedel in 1953 at the same time as the quadrupole mass filter.

Subsequent interest followed two lines: selective ion storage for the study of

18

ionic species, and methods to obtain a mass spectrum of the ions stored in the
trap. The long term storage of selected m/z values in the ion trap has allowed
studies of ion spectroscopy and other ionic properties. A “scanning" technique
has been developed by Stafford, et. al.22 (mass-selective instability scanning
mode) in which ion trajectories are destabilized in sequential order of their m/z
values. A fraction of the destabilized ions pass through one of the end caps
behind which is an ion detector. The plot of ion current as a function of the m/z
value being destabilized is a mass spectrum. The capabilities of the ion trap
have developed rapidly. This progress was greatly stimulated by the availability
of a powerful commercial (Finnigan MAT, San Jose, CA) ion trap mass
spectrometer (ITMS). Now in the hands of several innovative investigators, the
m/z range of the ITMS has been extended to 70,000 Da/z”, and the ITMS has
been operated at resolutions (FWHM) in excess of 100,000“.

Since the availability of the ITMS, many investigators have extended the
ion storage capabilities to a wide range of ionization techniques. These include

28 ’29 '30 31

electron impact ionization25 36, positive chemical ionization”. , negative

35

chemical ionization”, electrosprayaaia‘, ion spray”, thermospray37v38,

4O 41 ’42

atmospheric sampling glow discharge ionization”, laser desorption . , and

various photoionization techniques43 .44 :45 :46

. Ionization is either performed
within the trap, or outside the trap followed by ion injection into the trap. Thus,
the ion trap is rapidly developing as a storage ion source adaptable to a wide

variety of ionization methods.

19

The scan speed of the commercial ITMS instrument is 5,555 Da/s, or 117
ms per 650 Da scan. Full scan spectrum generation rates of greater than 5
spectra per second are difficult to achieve due to the need for ion generation,
collisional damping, and mass scanning in each scan cycle. Higher scan rates
are obtained only at the expense of mass resolution, mass range and sensitivity.
There are thus inherent limitations and trade-offs with the mass-selective
instability scanning method for achieving the mass spectra of the ions stored in
the trap.

When the ion trap is combined with external TOF mass analysis, most of
these trade-offs no longer apply. The mass resolution of the TOF system is not
dependent on the precision of the quadrupole field as is the ITMS when
operating in the mass-selective instability mode. Extraction pulses can be
applied more frequently than can destabilizing sweeps. The extraction is
complete in a few us and a new ionization/storage cycle can begin
simultaneously with the mass analysis of the previous batch. The resulting
higher spectral generation rate has the potential to increase the dynamic range
available and increase sample utilization efficiency by emptying the source

before it becomes space-charge limited with analyte ions.

20

1.4 Quadrupole ion trap] time-ot-flight mass spectrometer

Pulsed ejection with subsequent mass analysis of trapped ions has been
implemented before in several laboratories“7'48 ' ‘9 ' 5°. Information on the velocity
distribution of ions was obtained by this method, but work in this direction
stopped in the late seventies in favor of the rapidly developing selective
destabilization mode of mass analysis. The problem of achieving temporal
focusing of ions having a significant distribution of starting velocities and
positions is, if anything, exacerbated by the ion motion induced by the RF field
oscillations. In fact, much of the early work was an exploration of the optimum
phase angle of the RF field at the onset of the extraction ‘8' 49' 5°. Other studies
explored the cessation of RF altogether prior to extraction".

Recently, the quadrupole ion trap was interfaced with time-of-flight mass
spectrometry in Professor Lubman’s Lab“. The quadrupole ion trap is used as
an ion source for the preparation of ions to be analyzed by the time-of-flight
mass spectrometer. Ions generated by an external ionization method are
introduced into the quadrupole ion trap and accumulated in this ion source. This
ion source is filled with collisional bath gas. lens are trapped in this source up to
several hundreds of milliseconds. The ion displacements and initial kinetic
energies are minimized by collisional cooling with the bath gas during this
period. A good mass resolution with time-of-flight mass analysis is achieved by
extracting these “ion trap prepared” ions. Extensive collisional cooling is

necessary because the nonuniform extraction field generated by the hyperbolic

21

shaped electrodes of the ion trap is not compatible with the uniform, linear
extraction field required for the time-of-flight mass analysis. Good mass
resolution is only achieved by inserting an ion cooling operation in the spectrum
generation cycle. This sacrifices the fast spectral generation advantage of time-

of-flight mass spectrometry as well as the high sample utilization duty cycle.

1 .5 Segmented rlng Ion trap storage source/reflectron/tlme-ot-fllght

(SIRS/TOF) mass spectrometer

To make a ion storage source that will increase the duty cycle of the time-of-
flight mass spectrometer and meet the optical requirements of time-of-flight mass
analysis, a segmented ring, ion storage ion trap has been developed. The
theoretical development and computer simulation of this innovative ion source
for time-of—flight mass analysis is discussed in Chapter Two. To minimize the
detrimental effect due to the initial kinetic energy distribution, high extraction
voltages synchronized with the appropriate RF phase angle are required. This is
also discussed in Chapter Two. The development and the design considerations
of a reflectron that is able to focus ions extracted from the ion source with a wide
energy range distribution is discussed in Chapter Three. The instrument
construction, control and timing system, static and dynamic voltage supplies,
and the data acquisition and processing systems are described in Chapter Four.
Instrument performance, characterization of the ion storage of this segmented

ring ion trap, and the advantages of interfacing a gas chromatograph with this

22

novel ion storage source/reflectron/time-of-flight mass spectrometer are

discussed in Chapter Five.

References:

 

‘ Holland, J. F., Enke, C. 6., Allison, J., Stults, J. T., Pinston, J. 1)., Newcome,
B., and Watson, I. T.: Mass Spectrometry on the Chromatographic Time Scale: Realistic
Expectations, Anal. Chem. 55, 997A-915A (1983)

2 Gross, M. L., Rempel, D. L.: Science, 226, 261 (1984)

3 Cameron, A. E. and Eggers, D. F. Jr., Rev. Sci Instrument, 19, 605 (1948)

‘ Wiley, W. C. and McLaren, I. H.: Time-of-Flight Mass Spectrometer with
Improved Resolution. Rev. Sci. Instrument, 26, 1150, (1955),

‘ Gohlke, R. 8., Anal Chem, 31, 535 (1959)

‘ Wollnik, H.: Time-Of-Flight Mass Analyzer. Mass Spectrometry Reviews, 12,
89-114 (1993)

7 Ioanoviciu, 1)., Yechak G. E. and Enke c. G.: Second-Order Space-Time
Transfer Matrix of The Two Stage Electrostatic Mirror. Int. J. Mass Spectrom. 1011
Processes, 94, 281-291 (1989)

' Bosel, U., Weinkauf, it And Schlag, E. w. : Reflectron Time-of-Flight Mass
Spectrometry and Laser Excitation for the analysis of Neutrals, Ionized Moleclues and
Secondary Fragments. Int. J. Mass Spectrom. Ion Processes, 111, 121-166 (1992)

9 Walter, K., Boesl, U., and Schlag, E.W.: Mass Resolution of 10000 in a laser
ionization time-of flight mass Spectrometer. Anal. Chem, 57, 18844889 (1985)

10 Marable N. L. and Sanzone, 6.: High -Resolution Time—of—Flight Mass
Spectrometry Theory of The Impulse-Focused Tune-of-Flight Mass Spectrometer, Int. J.
Mass Spectrom. Ion Processes, 120, 97-100 (1993)

11 Eckenrode, B. A., Watson, I. T., and Enke CG. and Holland J. F.: Complete
Mass Spectrometry/Mass Spectrometry Data Field Acquisition on the Chromatographic

23

 

Time Scale by Time-Resolved Ion Momentum Spectrometry with Time-Array Detection,
Anal Chem. 62, 1362-1367 (1990)

‘2 Ben-Itzhak, 1., Carnes, K. D. And DePaola B. D.: Fast Timing Signal Sorter for
Multiple Hit Coincidence Time-of-Flight Spectroscopy, Rev. Sci. Instrum. 63, 5780-5783
(1992)

13 Holland, J. F., Newcombe, B., Tecldenburg, R. Jr , Davenport, M., Allison, J.,
Watson, J. T., Enke, C. G.: Design, Construction, and Evaluation of an Integrating
Transient Recorder for Data Acquisition in Capillary Gas Chromatography/I" 1me-of-Flight
Mass Spectrometry. Rev. Sci. Instrum., 1991, 62, 69-76 (1991)

1‘ Erickson, E. D., Yefchak, G. B., Enke C. G., and Holland J. F.: Mass
Dependence of Time-Lag Focusing in Time-of-Flight Mass Spectrometry — An analysis.
Int. J. Mass Spectrom. Ion Processes, 97, 87-106 (1990)

‘5 a. Mamyrin, B. A., Karataev, v. 1., Shmikk, D. v., and Zagulin v. A.: The Mass
Reflectron, A New Nonmagnetic Time-of-Flight Mass Spectrometer with High
Resolution. Sov. Phys. JETP, 37, 1, 45-48 (1973)

b. Mamyrin, B. A., and Shmikk, D. V.; The Linear Mass Reflection. Sov. Phys.
JETP 49, 5, (1979)

‘5 Stein, a: On Time Focusing and Phase Space Dynamics in Time-of-Flight Mass
Spectrometer Design. Int. J. Mass Spectrom. Ion Processes, 132, 29-47 (1994)

‘7 a. Kinsel, G. R. and Johnston, M. V.; Post Source Pulse Focusing : A Simple
Method to Achieve Improved Resolution in a Time-of-Flight Mass Spectrometer, Int. J.
Mass Spectrom. Ion Processes, 91, 157-176 (1989)

b. Kinsel, G. R., Mowry, C. D., McKeown, P. J. and Johnston, M. V.; Resolution
Enhancement in Linear Time-of Flight Mass Spectrometry by Post-Source Pulse Focusing,
Int. J. Mass Spectrom. Ion Processes, 91, 157-176 (1989)

1’ Yefchak, G. B., Enke, C. G. and Holland, J. F.: Models for Mass Independent
Space and Energy Focusing in Time-of-Flight Mass Spectrometer. Inter J. Mass
Spectrom. Ion Processes, 87, 313-330 (1989)

24

 

'9 Grix, R., Gruener, U., Li, G., Stroh, H. and Wollnik, H.: An Electron Impact
Storage Ion Source for Tune-of-Flight Mass Spectrometers. Int. J. Mass Spectrom. Ion
Processes, 93, 323-330 (1989).

”Mary Ann Seeterlin, Ph. D. Dissertation, Michigan State University, 1993

2' Studier, M. H.: Continuous Ion Source For a Time-of-Flight Mass
Spectrometer. Rev. Sci. Instrum., 34, 1367-1370 (1963) ,

’3 Stafford, G. C. (Jr), Kelley, P. E., Syka, J. E. P., Reynolds, w. B., and Todd, J.
F. J .: Recent Improvements in and Analytical Applications of Advanwd Ion Trap
Technology. Int. J. Mass Spectrom. Ion Processes, 60, 85-98 (1984).

’3 Kaiser, R. E. (Jr.), Cooks, R. G., Stafford, G. C. (Jr.), Syka, J. E. P., and
Hemberger, P. H.: Operation of a Quadrupole Ion Trap Mass Spectrometer To Achieve
High Mass/Charge Ratios. Int. J. Mass Spectrom. Ion Processes, 106: 79-115 (1991).

“Williams, J. D., Cox, K. A., Cooks, R. G., Kaiser, R. E. (Jr.), and Schwartz, J.
C.: High Mass-Resolution Using a Quadrupole Ion-Trap Mass Spectrometer. Rapid
Commun. Mass Spectrom., 5, 327-329 (1991).

2’ Eckenrode, B. A., McLuckey, S. A., and Glish, G. L.: Comparison of Electron
Ionization and Chemical Ionization Sensitivities in an Ion Trap Mass Spectrometer. Int. J.
Mass Spectrom. Ion Processes, 106, 137-157 (1991).

2‘ Loun's, J. N., Amy, J. w., Ridley, T. Y., and Cooks, R. G.: Injection of Ions into
a Quadrupole Ion Trap Mass Spectrometer. Int. J. Mass Spectrom. Ion Processes, 88, 97-
1 11 (1989).

2" Eckenrode, B. A., McLuckey, S. A., and Glish, G. 1.: Comparison of Electron
Ionization and Chemical Ionization Sensitivities in an Ion Trap Mass Spectrometer. Int. J.
Mass Spectrom. Ion Processes, 106, 137-157 (1991).

2' Mather, R. B., Lawson, G., and Todd, J. F. J.: The Quadrupole Ion Storage
Trap (Quistor) as a Low-Pressure Chemical Ionization Source for a Magnetic Sector Mass
Spectrometer. Int. J. Mass Spectrom. Ion Physics, 28, 347-364 (197 8).

’9 Brodbelt, J. S., Louris, J. N., and Cooks, R. 6.: Chemical Ionization in an Ion
Trap Mass Spectrometer. Anal. Chem, 59, 1278-1285 (1987).

25

 

3° Boswell, S. M., Mather, R B., and Todd, J. F. J.: Chemical Ionization in the Ion
Trap: A Comparative Study. Int. J. Mass Spectrom Ion Processes, 99, 139- 149 (1990).

31Ecltenrode, B. A., Glish, G. I... and McLuckey, S. A.: Negative Ion Chemical
Ionization in a Quadrupole Ion Trap Using Reagent Anions Injected From an External Ion
Source. Int. J. Mass Spectrom. Ion Processes, 99, 151-167 (1990).

32 Van Berkel, G. J., Glish, G. L., and McLuckey, S. A.: Electrospray Ionization
Combined with Ion Trap Mass Spectrometry. Anal. Chem, 62, 1284—1295 (1990).

33 Van Bcrkcl, G. J., McLuckey, S. A., and Glish, G. 1.,: Electrospray Ionization of
Porphyrins Using a Quadrupole Ion Trap for Mass Analysis. Anal. Chem, 63, 1098-1109
(1991).

3‘McLuckey, S. A., Van Berkel, G. J., Glish, G. L., Huang, E. C., and Henion, J.
D.: Ion Spray Liquid Chromatography/Ion Trap Mass Spectrometry Determination of
Biomolecules. Anal. Chem, 63, 375-383 (1991).

3’ Kaiser, R B. (Jr), Williams, J. D., Schwartz, J. C., Lammert, S. A., and Cooks,
R. G.: Thermospray LC/MS with a Quadrupole Ion Trap and Recent Applications of Ion
Injection. Presenwd at the 37th ASMS Conference on Mass Spectrometry and Allied
Topics, 369-370 (1989).

“Kaiser, R. E. (Jr), Williams, J. D., Lammert, S. A., Cooks, R. G., and Zakett,
D.: Thennospray Liquid Chromatography-Mass Spectrometry with a Quadrupole Ion
Trap Mass Spectrometer. J. Chromatog, 562, 3-11 (1991).

’7 McLuckey, s. A., Glish, G. 1., and Asano, K. G.: Coupling of an Atmospheric-
Sampling Ion Source with an Ion-Trap Mass Spectrometer. Analytica Chimica Acta, 225,
25-35 (1989).

3‘ a.Van Berkel, G. J ., Glish, G. L., and McLuckey, S. A.: Electrospray Ionization
Combined with Ion Trap Mass Spectrometry. Anal. Chem, 62, 1284-1295 (1990).

”Todd, J. F. J.,Mylchreest,1. C., Berry, A. J., Games, D. B., and Smith, R. D.:
Supercritical Fluid Chromatography/Mass Spectrometry with an Ion Trap Detector. Rapid
Commun. Mass Spectrom. 2, 55-58 (1988).

26

 

‘° Louris, J. N., Amy, J. w., Ridley, T. v., and Cooks, R. G.: Injection of Ions into
a Quadrupole Ion Trap Mass Spectrometer. Int. J. Mass Spectrom Ion Processes, 88, 97-
11 1 (1989).

“ Heller, D. N ., Lys, 1., Cotter, R. J., and Uy, O. M: Laser Desorption from a
Probe in the Cavity of a Quadrupole Ion Storage Mass Spectrometer. Anal. Chem, 61,
1083-1086 (1989).

‘2 Goeringer, D. B., Glish, G. L., Asano, K. G., and McLuckey, S. A.: Applications
of Laser Desorption in an Ion Trap Mass Spectrometer. Presented at the 37th ASMS
Conference on Mass Spectrometry and Allied Topics, 1260-1261 (1989).

‘3 Louris, J. N., Brodbelt, J. S., and Cooks, R. G.: Photodissociation in a
Quadrupole Ion Trap Mass Spectrometer Using a Fiber Optic Interface. Int. J. Mass
Spectrom Ion Processes, 75, 345-352 (1987).

“ Creaser, C. S., McCoustra, M. R S., and O'Neill, K 13.: Combined Gas
Chromatography/Tandem Mass Spectrometry Using Laser Photodissociation. Org. Mass
Spectrom., 26(4), 335-338 (1991).

‘5 Lifshitz, C.: Dissociative Photoionization in the Vacuum UV Region with Ion
Trapping. Int. J. Mass Spectrom Ion Processes, 106, 159-173 (1991).

“Goeringer, D. B., Glish, G. L., and McLuckey, S. A.: Fixed-Wavelength Laser
Ionization/Tandem Mass Spectrometry for Mixture Analysis in the Quadrupole Ion Trap.
AnaL Chem, 63, 1186-1192 (1991).

‘7 Mosburg Jr., E. R, Vedel, M. Zerega, Y., Vedel, F. and Anere, J.: A Tirne-of-
Flight Method for Studying the Properties of an Ion Cloud Strored in An RF Trap. Int. J.
Mass Spectrom Ion Processes, 77, 1-12 (1987).

‘8 Waldren, R M. and Todd, J. F. J.: The Quadrupole Ion Store (QUISTOR). Part
III. Studies on Phase-Synchronized Ion Ejection; The Effects of Ejection Pulse Width and
Detection Pulse Delay. Int. J. Mass Spectrom. Ion Phys. 29, 315-335. (1979)

‘9 Lawson, G., Bonner, R F. and Todd J. F. J.: The Quadrupole Ion
Store(Quistor) as a Novel Source for a Mass Spectrometer, J. Physics E: Scientific
Instruments, 6, 357-362 (1973)

27

 

5° Brincourt, G., Catella, R., Zerega, Y. and Andre, J.: Time-of—flight Detection of
Ions Ejected from a Radio Frequency Quadrupole Trap: Experimental Determination of
Their fz Secular Frequency, Chemical Physics Letters, 174, 6, 626-630 (1990)

5’ a. Michael, S. M., Chien, B. M., and Lubman, D. M.: An Ion Trap Storage
IT ime-of-Flight Mass Spectrometer. Rev. Sci. Instrum. 63, 4277-4284, (1992).

b. Chien, B. M., Michael, S. M. and Lubman, D. M.: Enhancement of Resolution
in Matrix-Assisted Laser Desorption Using an Ion-Trap Storage] Reflectron Time-of-
Flight Mass Spectrometer. Rapid Comm. Mass Spectrom 7,837-843 (1993).

c. Chien, B. M., Michael, S. M. and Lubman, D. M.: Plasma Sorn'ce Atmospheric
Pressure Ionization Detection of Liquid Injection Using an Ion Trap Storage/Reflection
Time-of Flight Mass Spectrometer. Anal. Chem. 65, 1916-1024 (1993).

d. Michael, S. M Chien, B. M., and Lubman, D. M.: Detection of Electrospray
Ionization Using an Ion Trap Storage/Reflectron Time-of Flight Mass Spectrometer. Anal.
Chem 65, 2614—2620 (1993).

e. Chien, B. M., and Lubman, D. M.: Analysis of the Fragments from Collision
Induced Dissociation of Electrospray-Produced Peptide Ions Using an Ion Trap
Storage/Reflection Time-of Flight Mass Spectrometer. Anal. Chem 66, 1630-1636
(1994).

f. Qian, M.; Lubrmn, D. M.: Analysis of Tryptic Digests Using Michrobore HPLC
with an Ion Trap Storage] Reflectron Time -of-Flight Detector. Anal Chem. 67, 2870-
2877 (1995)

g. Lee, H., Lubman, D. M.: Sequence-Specific Fragmentation Generated by
Matrix-Assisted Laser Desorption/Ionization in a Quadrupole Ion Trap] Reflectron Time-
of-Flight Device. Anal Chem. 67, 1400—1408 (1995)

b. He, L., Liang, L., and Lubman, D. M.: Continuous-Flow MALDI Mass
Spectrometry Using An Ion Trap] Reflectron Time-of -Flight Detector. Anal Chem. 67 ,
4127-4132 (1995)

Chapter 2 Theoretical development and computer simulation of
the segmented ring ion trap source for time-of-fllght mass

spectrometry

2.1 Background

The concept of using an ion trap as an ion storage source for time-of-flight mass
spectrometry has existed in Professor Enke's group for several years. In 1991,
Paul Vlasak and Professor Enke submitted a grant application for the
development of a quadrupole ion trap/time-of-flight mass spectrometry system as
part of the NIH/MSU Mass Spectrometry Facility renewal proposal. During the
summer of 1992, Professor Enke, Professor Holland and I started to work on a
revised version of this grant application to be submitted as a independently-
funded project. The idea of using a segmented ring ion trap storage source for

the time-of-flight mass spectrometer was delineated at that time.

2. 1. 1 Quadrupole ion trap

A suitable electrode configuration for trapping ions is the quadrupole ion trap
which is composed of a hyperbolic ring electrode located between two
hyperbolic end caps. This arrangement was first proposed by Paul and
Steinwedel in 19561 .The general geometry of the device is described by the
relationship

’02 = 22:

28

filer

bill

if

wile

will
for

29

where r0 is defined as the radius of the ring electrode and 220 is the separation
between two end-caps. A dynamic voltage is applied between the ring electrode
and the end caps. The resulting ion motion, resolved into r and 2 components,
can be represented by the Mathieu differential equation

%+(a.+2q.ws2rl.=o

in which x= ror z and
_ BeU
mroznz

49V
a: " .2qr " - ”1,0202 (0’

a2 = —2a, =

where Vis the RF voltage (zero to peak), 9 is the RF frequency and U is the DC
voltage between the ring and cap electrodes. The parameters a and q defined
above determine whether the ion trajectory is stable (bound) or unstable
(unbounded). Regions of stability may be plotted in (a, q) space giving a stability
diagram as shown in Figure 2-13.

Iso-ji lines are also shown in Figure 2-1. The significance of the
parameter [3 is that it is related to the frequencies of ion motion. [3 is a parameter
which only depends on the value of a and q. It can be shown that the ion motion
has a fundamental or “secular” frequency of oscillation oh and a number of

higher order components of frequency or. given by

mn=(2n+B)%,n=0,1,2 ......

a:
0.2
,6 034 a o ,. q,=0.9oa
0 0.5” l“ /
0.4 /‘ /
I

 

 

--0.6 T ' \\\\r'

“0.7 - Jr :— i : UL T T: q:
l 0.2 0.4 0.6 0.3 1.0 1.2 1.4 1.6

 

Figure 2-1. Stability diagram for the three-dimensional quadrupole ion trap.

lie
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(lei:
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31

The solution to the Mathieu equation allows stable motion only for 8 values
between 0 and 1. Hence, the two sets of intersecting lines in Figure 2-1
represent frequencies of the ion motion along the two perpendicular r and z axes
and are denoted by Band B, which is related to the oscillating frequency in the
two dmensions or, (a.

The Mathieu equation assumes that there is only one ion in the trap. Also
the equation assumes that the hyperbolic electrodes are perfectly shaped and
positioned. In practical cases, a considerable amount of space charge exists in
the trap and this alters the potential field within the ion trap.

Dawson and coworkers2 developed a pseudopotential-well method
describing the ion motion in the quadrupole ion trap. Disregarding the trajectory
ripple arising from higher order oscillations, ions exhibit simple oscillatory motion
at secular frequencies 01),, drain a so-called pseudopotential well of depth D, and
D, as described in Figure 2-2.

9V2

0 =-
’ 4mz§n2

 

D2 = 20,
This model has been used to calculate the maximum ion density N.,... in the ion

trap when the space charge effect is considered”.

3 m2
Nm-64lt[ 92}:

3( v2 \
Nm=4rt mflzr‘
K 0 /

 

 

 

32

\
a ........................... V /
r///_._‘+ >
/ X‘
l (Dz )
\, 1’.
\ 7 .
announce-.v-cscanu’z’.unu'o-c.%“~\
//// \\ .g '
N.
I (D I
l l'
\» J D
\\> _I r
.\\ I“,
\x._./;". ....................................

Figure 2-2. Representative diagram of the parabolic pseudopotential well
Dr and Dz.The respective secular frequencies of ion oscillation within the
wells are to, and 05,,

If I
ma
Ice;

Ire:

2.1
in
eler
arc“
qta

lllll‘l

33

If the ion trap is operated under conditions which maintain a constant V, the
maximum ion density is inversely proportional to the mass and frequency. If qz is

kept constant, the maximum ion density is proportional to the mass and the RF

frequency.

2. 1.2 Cylindrical ion trap

An ion storage device of cylindrical geometry is one in which a cylindrical barrel
electrode of radius r1 replaces the hyperbolic surface ring electrode of radius rs
and two planar disk (end cap) electrodes replace the end-cap electrodes of the
quadrupole ion trap. The distance between the planar disks is 221, while the
minimum separation between the end-cap electrodes of the quadrupole ion trap
is 220. A patent for a cylindrical ion trap was issued to Langmuir et al. in 1962‘.
With some mathematical approximations, Benilan and Audoin5 deduced that
ionic motion in the cylindrical ion trap may be described by the Mathieu equation

with aand qreplaced byctand 1, given by
- [12 _ £2
a—az(n)tx-Qz(r1)

The theoretical stability diagrams of the two different geometries r,=z,, and
r,2=&,2, were obtained by numerically calculating ion trajectories, using the
Runge-Kutta method of integration, and were compared with that of the
quadrupole ion trap. These stability diagrams involving the or and x parameters
for these two cylindrical ion traps are very similar to the stability diagram based

on a and q for the quadrupole ion trap”. Bonner et al.‘3 discussed the theoretical

34

aspects of the cylindrical ion trap with RF applied to the ring electrode and
presented first experimental evidence of ion storage in a cylindrical ion trap. For
a cylindrical ion trap with the geometric relationship r3 =22f, the potential
distribution is

_ (-1)" laanr)
vlr.2)-4%2(2~+ 1):: lo(Pnr,)°°s(p"z)

n

_ (2n+1)1t
pn _ 221

 

where la is a zero-order modified Bessel function of the first kind. In the case of
the quadrupole ion trap, the electric fields in the rand z direction depend only on
r and 2 respectively; thus the fields and the equations of the ion motion are
uncoupled. In the case of cylindrical ion trap, both the fields and the equations of
the ion motion are coupled. However, by a numerical calculation method, Bonner
et al. found that the equipotential fields between the quadrupole ion trap and the
cylindrical ion trap were quite similar. This provided an explanation for the ion
storage characteristic within the cylindrical ion trap. Mather et al.7 determined
experimentally the stability diagrams of three cylindrical ion traps with the
geometric ratios of rf/zf of 1.476, 1.966, and 1.766. The RF frequency was
fixed. The boundary RF voltages with regard to different DC offset voltage
settings were determined according to the existence of Ar“ stored in these
cylindrical ion traps. They concluded that the experimental results were in broad
agreement with theoretical calculations allowing for some possible distortion due

to the space charge effect caused by multiple ions present in the trap.

35

2. 1.3 Segmented ring ion trap

The segmented ring ion trap is developed to be an ion storage source for the
time-of-flight mass spectrometer“. It consists of two flat end plates and a stack of
ring diaphragms instead of one center ring electrode as in the quadrupole ion
trap or cylindrical ion trap. Each of the end plates has a center hole space
covered with a mesh screen to allow ion transmission. The inside diameter of the
ring electrode is defined as Zr; and the distance between two end plates is
defined as an. Theoretically, the potential field of the cylindrical ion trap could
be achieved perfectly by the segmented ring ion trap as the space between each
diaphragm is decreased and the number of ring diaphragms is increased. For
electronic circuit simplicity, the number of ring diaphragms composing the ring
electrode in our segmented ring ion trap is minimized to two. The ion storage
characteristics and the time-of-flight mass analysis characteristics of this

segmented ring ion trap source were first examined by computer simulation.

2. 1.4 Computer simulation

In 1968, a numerical calculation was used by Dawson and Whetten“ to analyze
single ion trajectories in the quadrupole ion trap. Benilan and Audoin‘5 used a
numerical method to solve the Laplace equation to calculate the potential field of
cylindrical ion traps and an ion trap with spherical and caps and a ring electrode
of circular cross section. Since then, computer simulation has been widely used
to simulate the behavior of ion storage, mass selective isolation, ion collisions

with the bath gas and the effect of nonlinear resonance in the quadrupole ion

36

trap. March at al.” developed a computer simulation program called SPQR
(specific program for quadrupole resonance) which uses a field interpolation
method and is able to simulate the mass selective isolation and resonance
excitation of ions stored in the quadrupole ion trap. The ITSIM simulation
program11 developed at Purdue University is able to simulate the behavior of a
large number of ions in the different ITMS operation modes. The effects of space
charge and bath gas collision are considered. The imperfection of the electrode
geometry of a real ion trap mass spectrometer is accounted for by expanding
electric field equations to also include higher-order terms based on Legendre
polynomials. Franzen12 simulated ion behavior when multipole fields are
superimposed on the quadrupole field.

SIMION13 is a computer program developed by Dahl and Delmore.
Iterated numeric calculation gives the ion trajectories under the electric field
generated by any specified arrangement of electrodes. Ma et al.14 demonstrated
the application of SIMION for the simulation of quadrupole ion trap operation.

The electric field resulting from a cylindrical ion trap or the segmented
ring ion trap is much more complex than the quadrupole field. The superimposed
multipole field of the segmented ring ion trap is difficult to describe 0r solve
mathematically. SIMION can generate the electric field directly from the
electrode geometry. For the development of the segmented ring ion trap,
SIMION was used to compare the ion storage characteristics of the quadrupole

ion trap, the cylindrical ion trap and the segmented ring ion trap. SIMION was

37

also used to simulate the time-of-flight behavior of ions extracted from these

different ion trap geometries.

2.2 Theoretlcel development and computer slmulatlon of the segmented

ring Ion trap as an Ion trap storage deva

The electrodes of ion trap are represented by a set of point electrodes in
SIMION. The distance between the two flat end plates of the segmented ring ion
trap (SRIT) is 94 grid units which represents 9.4 mm (2r2 = 9.4 mm). The
conversion factor is 0.1 mm/grid. A cylindrical ion trap and a quadrupole ion trap
were also simulated. The cylindrical ion trap has the same conversion factor and
dimensions as the segmented ring ion trap. For the quadrupole ion trap, the
distance between the end caps is 57 grid units. A conversion factor of 0.1649
mm/grid was used to obtain the same 9.4 mm distance between two end caps.
The geometric configurations are is =2 r20, 2’, =2 r’, and 222 =2 Faforthese three
kinds of ion trap. A user program from David Dahl was modified to apply a
cosine function dynamic voltage and a DC offset to the ring electrodes. The end
caps (and plates) were set to 0 V. The time interval between each calculation is
less than 1 ns of ion motion. A time interval of 0.1 ns was employed in a few
instances for comparison. No significant difference in the ion trajectories was

noticed except the calculation time was increased dramatically.

38

2.2. 1 Computer simulation of the equipotential field of the ion traps

The SIMION program was used to obtain the equipotential field lines of the ion
traps. The voltage of both ring electrode elements was set at 300 V (Figures 2-4,
and 2-3(a)) or 350 V (Figure 2-3(b)). The end caps (end plates) were set at 0 V.
The equipotential lines (red lines) are voltages starting at 25 V and increasing in
25 V intervals. The equipotential lines are quite similar for the cylindrical ion trap
and the quadrupole ion trap. Because of the potential lines leaking into the
space between the two ring electrode elements, the potential lines inside the ion
trap are less dense for the segmented ring ion trap (Figure 2-3(a)) than for the
quadrupole ion trap(Figure 2-4 (b)) and the cylindrical ion trap (Figure 2-4(a))
when same amplitude of RF voltage is applied. This situation can be
compensated for by applying a higher voltage to the ring electrode elements in
the segmented ring ion trap. The potential lines generated in the segmented ring
ion trap with 350 V applied to the ring electrode elements (Figure 2-3(b)) are

quite similar to those in the cylindrical ion trap with 300 V applied (Figure 2-
4(a))-

2.2.2 Computer simulation of ion trajectories

Ion trajectory simulations were obtained by using SIMION with a modified user
program from Dahl“. The initial ion position was set at r=0.2r2 and Z=O.222. The
initial kinetic energy was set to 0 eV. The collision factor (MFP) was set to 4 x10'3
mm. The cosine wave RF frequency is 1.2 MHz and the RF voltage 300 V (zero

to peak). The positions in the r and 2 dimensions of an ion with m/z 100 in the

39

Ring electrode

1 l

End End
cap 689

 

 

 

 

 

(a) (b)

Figure 2-3. Equipotential contours of the segmented n'ng ion trap.
The red lines are equipotential lines starting 25 V in 25 V
increments. The endplates are 0 V and ring electrode is

300 V (a) and 350 V (b).

40

Ring
electrode

 

Ring
electrode

(a) (b)

Figure 2-4. Equipotential contours of (a) Cylindrical ion trap
(b) Quadruple ion trap.The red lines are equipotential lines
from 25 V to 275 V in 25 V intervals.

The end caps are 0 V and ring electrodes are 300 V.

$9

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41

segmented ring ion trap, cylindrical ion trap and quadrupole ion trap vs. storage
time are shown in Figures 2-5, 2-6, and 2-7. Although different degrees of
multipole fields exist in the cylindrical ion trap and the segmented ring ion trap,
the simulations clearly show that the ion motion characteristic of stable ion
trajectories are quite similar in all three ion traps. The fundamental frequency of
ion motion in the r dimension is 0.097 MHz for the segmented ring ion trap and
0.11 MHz for the quadrupole and cylindrical ion traps. The fundamental
frequency in the z dimension is 0.17 MHz for the segmented ring ion trap and
0.21 MHz for the quadrupole and cylindrical ion traps (Figures 2-5, 2-6, and 2-7).
The lower secular frequency of the segmented ring ion trap(Figure 2-5) is due to
the lower effective field strength in the trap as represented in the equipotential
contour. The ion displacements in the z and r dimensions are approximately 1.5
mm and 1.25 mm in all three ion traps.

The trajectories of ions of m/z 100 and 2000 in the segmented ring ion
trap are shown in Figures 2-8, and 2-9. The ion motion characteristic of this ion

trap is quite similar to that of the quadrupole ion trap.

2.2.3 Effect of initial phase angle of RF field on the ion motion

The effect of the RF phase applied when an ion was initially placed in the
segmented ion trap was examined. The ion position in the r and 2 dimensions
versus the ion storage time is shown for four different initial RF phase angles, 0,
1114, it and arr/4, as represented in Figures 2-10, and 2-11. The displacement in

the z dimension is about 2.5 mm for initial phases of RM and 3M4, 1.5 mm for

42

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Figure 2-8. Computer simulated ion trajectory of an ion of mlz 100
for an RF of 1.2 MHz and 300 V (zero to peak) in the segmented ring ion trap

46

 

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.. marremmmrsaass" a .:.aa::::::=" :-

       

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a
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E

Figure 2-9. Computer simulated ion trajectory of an ion of mlz 2000
for an RF of 1.2 MHz and 300 V (zero to peak) in the segmented ring
ion trap

47

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59¢ .69 £006 .0. 00005 ..E 05 .0065 0005 um 690:6 .32 .0 60.0.9.3 05.
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48

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ON

0.

.005 .0 .N... .o 0.0 000: 033
000.0 .00. 0.003 .0. 000000 “E 00.. 00.000 00000 “E 30.0.20 .30. .0 00.0.0000 000_
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Ion position in the r dimention (mm)

49

that of O, and 1.0 mm for that of 0. The displacement in the r dimension is 2.5
mm for initial phases of 0/4 and 30/4 and 1.25 mm for that of 0, and 1.0 mm for
that of 0. The fundamental frequency of ion motion is 0.17 MHz in the z
dimension and 0.097 MHz in the r dimension for all four initial phases. These
responses to the RF phase angle at the time of ion generation are similar to

those in the quadrupole ion trap’.

2.2.4 Relationship behveen the Ian kinetic energy and the RF phase

The ion's kinetic energy variations with the RF phase during the ion storage time
are shown in Figure 2-12. The ions that were generated at the cosine function
wave phases of 0/2 and 30/4 (red line and blue line) have more kinetic energy
variation than ions generated at the RF phases of 0 and 0 (black and green
lines). Ions generated at the RF phases of 0/2 and 30/4 normally have a kinetic
energy valley at the RF phases of n+(1/2)0 and a kinetic energy peak at the RF
phase of n0. Ions generated at RF phases of 0 and 0 normally have a kinetic
energy valley at the RF phase of n0 and a peak at the RF phase of n+(1/2)0.
Since the sample introduced into the segmented ring ion trap ion source
will remain in the source longer than the time period of one RF cycle, the sample
introduced over the entire RF cycle period can be ionized even through the
ionization occurs only during a fraction of the RF cycle period. Ions that are
generated in the ion source at a particular RF phase and analyzed at a related
RF phase, will be in their lowest kinetic energy position at the mass analysis

moment. To ionize the sample at a specific RF phase, the ionization energy

50

000.000 Sen .0 d... .o .0 000000 .. 303. 3000.00. 033 000 .0005 .00. 0.003 0......

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00000 ..1 00. 000 3.000 2.00... 00. 00. 0003.03 03002.03. 00... .N. -N 0.30.“.

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Ion kinetic energy [orbiltory un'rl)

51

could come from a pulsed laser beam or a pulsed electron beam. For the
segmented n'ng ion trap source with electron impact ionization design as
discussed in Chapter 4, electrons can only enter the ion source during half the
RF cycle. The effect of this “pulsed” ionization on the optimum RF phase at

which ions are extracted for TOF analysis will be discussed further in Chapter 5.

2.2.5 Stability diagram of the segmented ring Ion trap

The stability diagram of the segmented ring ion trap was constructed by
computer simulation following the same procedure which Mather et al.2 used to
determine the stability diagram of a cylindrical ion trap. An ion with mlz 100 was
placed in the segmented ring ion trap. The initial ion position was set at r=0.2r2
and 2:022... The dimensions of the ion trap are 222:9.4 mm and r22 =22}. The
initial ion kinetic energy and initial RF phase were set to zero. The ion trajectory
was considered stable if the ion remained in the segmented ring ion trap for 100
us. Ions that hit the electrode were considered unstable. The end plates were
set to O V. The DC offset applied to the ring electrode elements was varied from
~50 to 250 V. For each DC offset, the boundary RF voltage for a stable trajectory
was found using computer simulation.

The stability diagram expressed in DC offset voltage and RF voltage is
shown in Figure 2-13. For comparison, the equation used to calculate the a2 and
qzvalue for the quadrupole ion trap was used to calculate the stability diagram of
the segmented ring ion trap in 32 and q2 coordinates. The resulting stability

diagram is shown in Figure 2-14. The shape of the stability diagram is quite

50

100

(A) sdeo pue 01 peudde eBeuon 30

 

 

150

52

_. RFvoltage applied to
\ the ring electrode (V)
' l 1 l ‘\ l a I

400 1.600 800

 

  

Figure 2-13. Stability diagram of the segmented ring ion trap constructed
by computer simulation. The x axis and y axis show the RF and DC values of
the voltage applied between the ring electrode and the end plates.

53

02- a2

0.1- /

 

 

 

Figure 2-14. Stability diagram of the segmented ring ion trap constructed by
computer simulation. The a2 and a; values were calculated using the same
equation as that for the quadrupole ion trap.

54

similar to that of the quadrupole ion trap (Figure 2-1). When the DC offset of the
ring electrode elements is zero, the maximum boundary value of qz for the
segmented n’ng ion trap is 0.77 but for the quadrupole ion trap, the maximum
value of qz is 0.908. This difference indicates that the stable mass range of the
segmented ring ion trap is likely to be smaller than that of the quadrupole ion

trap when zero DC offset is used.

2.2.6 Effect of bath gas collisional cooling

For the development of a new ion storage device for a time-of-flight mass
spectrometer, the capability of ion storage is of greatest concern. The m/z range
of ions having stable trajectories is quite dependent on the actual physical
device and on the initial conditions when the ion is generated. These initial
conditions include the initial ion position in the ion trap, the initial ion kinetic
energy, initial direction of ion motion, and the initial RF phase when the ion is
generated. The space charge and collisional cooling effects play an important
role in ion stabilization. The collisional cooling effect of He bath gas was
simulated by SIMION with the user program. The program only simulates the
single ion situation. The collision frequency is determined by the mean free path.
The mean free path is generated from the random variation of a specified mean
free path factor which is pressure related. Collisions are assumed to be elastic.
After each collision, the ion loses a part of its kinetic energy; the fraction lost
depends on its own mass and the mass of the collision bath gas. Because the

source pressure is normally set at 1 x 1045 torr, the mean free path factor was set

55

at 4x10‘ mm which is approximately the mean free path value of a single ion at
room temperature when only thermal motion is considered. The collisonal
frequency is approximately 10 Hz at this pressure. However, the use of this
value only provides an idea of the effect of the bath gas collision and does not
necessarily represent the exact behavior at this pressure. During each collision
part of the ion's kinetic energy is transferred to the bath gas molecule.

The effects of collisional cooling on the ion position in r and 2 dimensions
vs. the ion storage time are shown in Figures 2-15 and 2-16. The RF voltage is
300 V (zero to peak) and 1.2 MHz. The initial ion position is r=0.2r2 and z=0.24.
The collision frequency is controlled by adjusting the mean free path factor. The
r and z dimension displacements decrease when the mean free path factor
decreases from 4x10310 40 mm which brings the mean time between collision to
around 10 us. As the mean free path factor decreases from 4x10‘ mm to 4x103
mm (which corresponds to a mean time between collision of 1000 us), there is
no significant effect on the ion trajectory during 100 pa storage period. This
shows that it is not possible to use the collision cooling effect to decrease the ion
displacement in the ion trap on the 100 us time scale. To achieve multiple
collisions within this interval would required an impractical high pressure. Even

then, ions generated late in the storage cycle would still not be cooled.

2.2. 7 Conclusion

The computer simulation studies of the segmented ring ion trap have shown that

the segmented ring ion trap has ion storage characteristics similar to the

56

CO?

on

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Ion Position in the r dimension (mm)

57

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58

quadrupole ion trap. The storage mass range may be somewhat smaller than
that of the quadrupole ion trap due to both the distortion of the quadrupole field
and a less effective RF field inside the trap. Nevertheless it appears likely that
an ion trap with this simple geometry will provide ion storage for subsequent

time-of-flight mass analysis.

2.3 Development and computer simulation of the segmented ring ion trap

as an ion source for time-0f-flight mass spectrometry

For the ion trap to be used as an ion storage source for time-of-flight mass
spectrometry, a pulsed voltage is applied to the end caps (and/or ring electrode)
during the ion extraction for the time-of-flight analysis event. The extraction field
generated in the ion trap source is one of the key factors affecting the sensitivity
and resolution of time-of-flight analysis. To develop an effective ion source for
time-of-flight mass spectrometry, computer simulation was used to evaluate the
ion extraction characteristics of the segmented ring ion trap and the quadrupole

ion trap.

2. 3. 1 Computer simulation of ion extraction from the quadrupole ion trap

storage source for time-of-fiight mass analysis.

The characteristics of ion extraction from a quadrupole ion trap were examined
with SIMION. The ion trajectories (green lines) for ions extracted from the
quadrupole ion trap as well as the equipotential contours (red lines) when an

800 V extraction pulse was applied between the rear and front caps of these ion

59

traps are shown in Figures 2-17, 2-18, and 2-19. When a 400 V pulse was also
applied to the ring electrode as shown in Figure 2-18, a set of a collimated ion
trajectories was obtained from the ions located in the back half of the ion trap at
the time of extraction. When the ring electrode voltage is 800 V (Figure 2-17) or
0 V (Figure 2-19), a set of very dispersed ion trajectories resulted. The lens
effect of the curved extraction fields is the major reason for the dispersed ion
trajectories. The unbalanced extraction voltages applied to the ring electrodes in
Figure 2-17 and Figure 2-19 result in a much more severe lens effect than in
Figure 2-18. The large ion trajectory dispersion will result in a high proportion of
ion loss during the time-of-flight mass analysis period.

The patterns of ion extraction trajectories vary with the RF applied to the
ring electrode. If the RF is not blocked at the time of extraction, a large
percentage of ion loss during the time-of-flight mass analysis is expected. In the
grant proposal for this project to NIH in 1991, we proposed that for time-of-flight
analysis from the quadrupole ion trap storage source, the best results will be
obtained by setting the ring extraction potential at a potential half way between
the extraction potential of two end caps.

This most favorable situation for ion extraction from the quadrupole ion
trap was modeled in more detail as shown in Figure 2-20. The distance between
the two end caps of the quadrupole ion trap is 20 grid units and the conversion
factor is 1.0 mm/grid (Figure 2-20). Several additional electrodes were added at

the front of the ion trap to simulate the ion acceleration and focusing electrodes.

60

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62

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64

Ions of mlz 100 are initially placed in the quadrupole ion trap in an X pattern.
The green lines are the ion trajectories. The ion positions at every 0.5 ps interval
of flight time are represented by the red dots. The field along this flight path is
produced by the ion trap extraction potential and a second acceleration
electrode as in the design of Lubman“. The progression of the groups of dots
representing the same flight time and relative distance over which they are
spread clearly indicates that a spatially compact ion bunch is not achieved.
Computer simulation shows that it is not possible to find a position along the
flight path where the flight time of isomass ions is closely the same. The
convergence position of ion trajectories depends on the position of the ion in the
source at the moment of application of the extraction pulse. The minimum ion
package temporal dispersion is approximately 500 ns.

As discussed in chapter one, a small minimum value of temporal
dispersion of isomass ions at the space focus plane is critical to achieve good
mass resolution with time-of-flight mass analysis. The simulation above clearly
indicates that good mass resolution could not be achieved by extracting ions
from the quadrupole ion trap unless the ions are initially located very close to the
center region of the trap when the extraction pulse is applied. This initial
condition could be achieved by using extensive collisional damping with He bath
gas but this will require many milliseconds of cooling time“. Thus good
resolution is only obtained by sacrificing the advantage of the high spectral

generation rates that can be provided by the time-of—flight mass spectrometer.

65

2.3.2 Computer simulation of ion extraction from the segmented ring ion

trap

For ion extraction from the segmented ring ion trap, the ring electrode elements
and the rear cap are given extraction voltages linearly proportional to their
distances from the exit cap. The equipotential contours of the segmented ring
ion trap when the extraction voltages are applied are shown in Figure 2-21. The
uniform extraction field allows ions at different radial positions to experience the
same extraction field profile. The ion trajectory simulation of the ions extracted
from the segmented ring ion trap is shown in Figure 2-22. The distance between
the rear cap and the exit cap for the segmented ring ion trap is 40 grid units
which represents a practical geometry of 9.4 mm separation; the conversion
factor is 0.235 mm/ grid. One additional electrode was placed in the front of the
ion trap to provide an ion acceleration voltage. In this case, the field along the
flight path consists of the linear ion extraction field generated inside the
segmented ring ion trap and the accelerating field experienced by ions exiting
the ion trap. The extraction field and acceleration field strengths are the same so
they form a single uniform extraction field. The ions are initially placed in the trap
in an X pattern. The green lines are ion trajectories and the groups of red dots
are ion positions as ions move along their flight path every 0.05 us. The isomass
ions are extracted from different initial positions in the segmented ring ion trap
but they converge to a very close pattern, spatially and temporally, at the space

focus plane (SFP). A minimum temporal dispersion of approximately 8 ns is

615 V 185 V
Ring Ring
electrode electrode
800 V element element 0 v
i l l r i l _
j 1' gig; Ion exrt
‘ i ' “ end cap

Rear
end cap

    

 

 

 

 

g.
H;
l i r l l!

Figure 2-21. Equipotential contours of the segmented ring ion trap
during the ion extraction. Electrodes are in black, the red lines are
equipotential lines from 50 V to 750 V in 100 V intervals.

67

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68

obtained. This small temporal dispersion at the space focus plane will result in

good resolution for time-of-flight mass analysis.

2.3.3 Proposed energy focusing method for tlme-of-fllght mass

spectrometer analysis from the Ion trap storage source

2.2.3.1 Strong extraction field

The extraction simulation above assumes a zero initial kinetic energy of the ion
extracted for time-of—flight mass analysis. As discussed in chapter one, another
contribution to the temporal ion spread at the SFP is the ion turn-around time in
the ion source. In order to minimize the ion turn-around time, a strong ion
extraction field is required. For a conventional time-of—flight mass spectrometer,
the space between the extraction grids is 2-4 mm and the extraction voltage
used is 200 to 400 V. For the segmented ring ion trap, an extraction voltage as

high as 800 V is required to achieve the same ion extraction field strength.

2.3.3.2 Synchronized ion extraction with RF phase

The kinetic energy of the ion at the time the ion extraction pulse is applied
determines the initial ion kinetic energy for time-of—flight analysis. The kinetic
energy of ions in the segmented ring ion trap varies with the RF phase and is
also a function of the phase at the time of ion generation. The ions at the RF
phases of 1:12 and 30/4 have wider kinetic energy variation than ions generated
at RF phases of 0 and 1: as shown in Figure 2-12. For minimum ion kinetic

energy, the extraction pulse should be applied at the moment of lowest initial

Q)
j

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A

diSCu:
lactic

which

CEDEEr

69

kinetic energy for ions generated at RF phases of rc/2 and 31t/4. The valley of the
kinetic energy of ions generated at RF phases n/2 and 31r/4 is at RF phases n/2
and 31r/4 degrees. So the extraction pulse should be applied at RF phases n/2 or
31r/4 if ions are generated throughout the RF cycle.

If ions are generated at a particular RF phase, then ion extraction should be
applied at the RF phase when the ions are at their lowest kinetic energy. As
discussed in Chapter 4 and Chapter 5, ions are generated only during some
fraction of the RF cycle and the mass resolution is related to the RF phase at

which the extraction voltage is applied.

2.3.3.3 Broad range energy focusing reflectron

In many time-of-flight mass spectrometers, a reflectron is used to image the
temporal ion package at the space focus plane on the surface of the detector.
Because of the reflectron, the total flight time is increased 2 to 4 fold within the
same physical dimensions of the vacuum chamber. The conventional reflectron
is built with a one or two stage linear static fields and the ion packet at the space
focus plane has a small kinetic energy variation. For ions extracted from the
segmented ring ion trap, a broader kinetic energy distribution than that produced
by most time-of-flight sources is expected. The ions generated away from the
center of the ion trap will have substantial energy due to the RF field applied
during the ion storage period and also the ions gain a broader extraction energy
during the ion extraction process due to the higher extraction voltage applied.

Thus, for time-of-flight mass analysis from the segmented ring ion storage

source
ions a
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70

source, It was necessary to develop a reflectron which could image the isomass
ions at the surface of the ion detector, and which would have a broader kinetic
energy tolerance. The reflectron development is described in the next chapter.

References:

 

1 Paul, w., Steinwedel, H.: A new Mass Spectrometer without a Magnetic Field. Z.
naturforsch. 8a, 448-50 (1953)

2 Dawson, P. H.: Quadrupole Mass Spectrometry and Its applications, Elsenver-
Amsterdam, Chapter 4, (1976)

3 March, R. E., Hughs, R. J.: Quadrupole Storage Mass Spectrometry, p192. John
Wiley and Sons, New York (1989)

4 Langmuir, D. B., Langmuir, R. V., Shelton, H. and Wuerker R. F., U.S. Patent No.
3, 065640 (1962)

5 Benilan, M. -N. and Audoin, C., Int. J. Mass Spectrom. Ion Phys.: Confinement
D’ions Par Un Champ Electrique De Radio-frequence Dans Une Cage Cylindrique. 11,
421-432 (1973)

6 Bonner, R. F., Fulford, J. 13., March, R. E., and Hamilton, G. F.: The Cylindrical
Ion Trap. Part I. General Introduction. Int. J. Mass Spectrom Ion Phys. 24, 255-269
(1977)

7Mather, R. B., Waldren, R M., Todd, J. F., and March, R. E.: Some Operational
Characteristics of a Quadrupole Ion Storage Mass Spectrometer Having Cylindrical
Geometry. Int. J. Mass Spectrom. Ion Phys., 33, 201-231 (1980)

8 Ji, Q., Vlasak, P. R., Holland, J. F., and Enke, c. (3.: A Segmented Ring Ion Trap
Storage Time-of-Flight Mass Spectrometer. (Proceedings of the 42nd ASMS Conference
on Mass Spectrometry and Allied Topics, Chicago, IL, May 29 - June 3, p. 1042, (1994)

9 Dawson, P. H. and Whetten, N. R.: J. Vac. Sci. Technol., 5, 1 (1968).

1° a. Londry, F. A., Roland, L. A. and March R. E.: Computer Simulation of Single
Ion Trajectories in Paul-Type Ion Traps. J Am Soc. Mass Spectrom. 4, 687-705 (1992)

f

b. .
StitCll‘
Mass S
c. .
of ions
Isolatic
d
Vodcl
Inlmdu
Pmccss

C..

lASMs

71

 

b. March, R. E., Londry, F. A., Alfred, R. L., Franklin, A. M. and Todd J. F.: Mass-
Selective Isolation of Ions Stored in a Quadrupole Ion Trap: A Simulation Study. Int. J.
Mass Spectrom Ion Processes. 112, 247-271 (1992)

c. March, R. E., Tkacyzk, M., Londry, F. A., Alfred, R. L.: Mass-Selective Isolation
of Ions Stored in a Quadrupole Ion Trap. Part 2. A Simulation Study of Consecutive
Isolation. Int. J. Mass Spectrom Ion Processes. 125, 9-32 (1993)

d. March, R. B., Londry, F. A., Alfred, R. L., Todd, J. F., Penman A. D. Vedel F. and
Vedel M.: Resonance Excitation of ions stored in a Quadrupole Ion Trap Part 111
Introduction to the Field Interpolation Simulation Method. Int. J. Mass Spectrom Ion
Processes. 110, 159-178 (1991)

e. March, R. B., McMaon, A. w., Allinson, E. T., Londry, F. A., Alfred, R. L., Todd
J. F., Vedel F.: Resonance Excitation of Ions Stored in a Quadrupole Ion Trap Part II.
Fin-titer Simulation Studies. Int. J. Mass Spectrom Ion Phys, 99, 109—124 (1991)

f. March, R. B., McMaon, A. W., Londry, F. A., Alfred, R. L., Todd, J. F., Vedel F.:
Resonance Excitation of Ions Stored in a Quadrupole Ion Trap Part I. A Simulation
Study. Int. J. Mass Spectrom Ion Proc., 95, 119-156 (1989)

1‘ a. Reiser Hans-Peter, Julian, R. K. and Cooks, R. G.: A Versatile Method of
Simulation of the Operation of Ion Trap Mass Spectrometer. Int. J. Mass Spectrom Ion
Processes. 121, 49-63 (1992)

b. Julian, R. K., Nappi, M., Well C. and Cooks, R. G.: Multiparticle Simulation of Ion
Motion in the Ion trap Mass Spectrometer: Resonant and Direct Current Pulse Excitation.
JASMS, 6, 51-70 (1995)

‘2 Franzen, J.: Simulation Study of an Ion Cage with Superimposed Multipole Fields.
Int. J. Mass Spectrom Ion Processes. 106, 63-78 ( 1991)

‘3 SIMION 4.0 Dahl, D. A., and Delmore J. E. , EG&G Idaho, Inc

1‘ Ma C., Lee H. and Lubman D. M.: Computer Simulation of The Operation of a
Three-Dimensional Qudrupole Ion Trap. Applied Spectroscopy, 46, 12, 1769-1779 (1992)

1’ Michael, s. M Chien, M., and Lubman, D. M.: An Ion Trap Storage ITthJe-of-
Flight Mass Spectrometer. Rev. Sci. Instrum. 63, 4277-4284, ( 1992).

Spec

1 fou

Chapter 3 Theoretical development and computer simulation of a
broad energy range focusing reflectron for a time-of-flight mass

spectrometer

3.1 Background

As discussed in chapter two, it was realized that it was necessary to design a
reflectron that is able to focus isomass ions with a broad kinetic energy
distribution that results from using the segmented ring ion trap as the ion storage
source. Rockwood1 postulated that a reflectron with a hyperbolic field will give a
perfect temporal focus for isomass ions starting at the same position with
different initial kinetic energies. This hypobolic reflectron field only applies to a
time-of-flight mass spectrometer with no field-free region. The mathematical
solution of the voltage profile for a reflectron in a time-of-flight mass
spectrometer with a field-free region is difficult to derive. In the summer of 1993,
I found an alternative numerical method to obtain a reflectron voltage profile for
a reflectron that can temporally focus isomass ions with a broad energy
distribution. Using this design approach, Paul Vlasak developed a reflectron for
the tandem time-of-fiight mass spectrometer in Professor Enke's lab and
obtained experimental verification?

An electrostatic reflectron system was first introduced by Mamyrin et al.3
for the time-of-flight mass spectrometer to focus an isomass ion bunch at the

detector position. The most commonly used reflectron has one or two linear

72

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betw
stag.

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two-s
iraler
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73

reflectron fields, and provides first order or second order energy compensation,
respectively. Homogeneous electric fields are generated by using mesh screens
between regions of different field strength. The mathematics of the one or two-
stage reflectron is well defined when only the initial kinetic energy distribution of
these isomass ions was considered" ‘. A high mass resolution (over 10000
FWHM) for a reflectron time-of-flight mass spectrometer has been obtained by
using laser ionization to achieve a minimal space and energy distribution of ions
at the moment of ion generation’.

The use of mesh screens to generate homogeneous fields for a one or
two-stage reflectron reduces ion transmission and can cause deviation in ion
trajectories. When an acceleration field was introduced into the reflectron
construction, the ion transmission was improved about 20%“. Wollnik et al.
studied the field distortion near the aperture of the mesh screen when a grid is
used to split two regions of different field strengths along the ion flight path. The
strong electric field reaches through the meshes of the grid generating a
multitude of small lenses. These small lenses modify an incoming parallel beam
so that some of the ion trajectories are strongly inclined to the beam axis and
easily miss a final ion detector7 . Several grid-free reflectrons have been
designed and a mass resolution about 10000 has been achieved“.

A reflectron with a single stage and a single grid at the front electrode has
been shown to be able to focus isomass ions with a 7% energy distribution while

maintaining a the resolving power up to a few thousand“. An energy range

74

greater than 10% has been temporally focused with a gridless reflectron in a
time-of-flight mass spectrometer”. Recently, because of the requirement for
focusing both precursor ion and secondary ions for the tandem time-of-flight
mass spectrometer, the energy range that needs to be focused has increased up
to 50% and more”. Cotter et al. have constructed a reflectron with 68
electrodes, the front electrode made of 90% transmission mesh screen. This
reflectron is able to focus all of the product ions simultaneously. The voltage
profile was determined experimentally by tuning the potentiometers between
each electrode and a curved voltage profile was obtained experimentally".
Derrik et al. discussed theoretically the fundamental limitations of the quadratic-
field reflectron for the temporal focusing of fragment ions with a broad energy
distribution”. Actually, the reflectron profile they discussed is the same as the
reflectron profile proposed by Rockwood in 1986, so it, too, requires a flight path
with no field free region.

The method of reflectron design | conceived is to calculate the reflectron
field numerically rather than to obtain a mathematical solution of the voltage
profile. This method allows an high orders of energy focus according to the
practical design parameters such as the length of the field free flight region, the

ion energy range needed, and the length of the reflectron.

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3.2. Mathematical consideratlons

3.2. 1 Temporal focuslng of lsomass lens that start at the same posltlon but

have different klnetlc energles.

The goals for using a reflectron in the time-of-flight mass spectrometer are to
increase the total flight time as well as to get isomass ions to reach the detector
at the same time. For the isomass ions that start at the space focus plane with
different initial kinetic energies (different initial velocities), the total flight time for
each ion to reach a detector position should be equal. The mathematical
equation describing the total flight time is

neon", (3-1)
The term T.,. is the total flight time of a single ion, T, is the flight time the ion
spends in the field-free region and T, is the flight time of the ion in the reflectron.
We want T... to be the same for ions with the same m/z value. This is
accomplished by choosing an appropriate potential profile for the reflectron.

An ion with a given kinetic energy will be slowed down after it enters the
reflectron. The kinetic energy of the ion is converted into potential energy. When
all of the kinetic energy of the ion has been converted into potential energy, the
ion stops. Then it is accelerated in the reverse direction. Its potential energy is
now reconverted into kinetic energy. For the following discussion, an ion with a
single positive charge is used. As described in Figure 3-1, an ion that stops at
position x... in the reflectron will have a maximum potential E(xm). This potential

energy is equal to the initial kinetic energy of the ion. After reconversion into

 

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77

kinetic energy, the ion is returned to the field free region with its initial kinetic
energy, only the directional vector has been altered.

The flight time the ion spends in the reflectron is

T521"?-

0 V. (3.2)

where v, is the ion velocity at position xin the reflectron and m is the ion mass,

 

 

2
v.=J;lE(x.)-E(x)1 (3.3)
The flight time in the field-free flight region is
L, + L, _ 5'.
T” - V - V (3'4)

where v.,, is the initial velocity of the ion and its velocity in the field-free region
and L, is the total length of the field-free region both before (L,) and after (L4)

the reflectron.

v," = "in? E(x,,,) (3.5)

So the total flight time is

Tlot = 7:1 + Tr (3-6)

x. W +
T”, =2I° T-i-b'v—Li (3.7)

Mathematically, we need to find a reflectron field E(x)=f(x) that will give
the same constant T.,. for isomass ions over a wide range of initial kinetic

energies.

 

The ‘
the l

iner

legit

illus-

78

One special case is when there is no field-free region (LFO), Then a
potential profile with an hyperbolic function will give a satisfactory solution.

For E(x)=ax’+b, and Ln=0

T”, = 21:53 (3.8)

X

T,,,=2Io"' dx (3.9)
12—; [E(x)— Erxn

 

 

T =21“ (3.10)

J25 [(5092" b)- --(ax2 bl]

T = 3.11
a. 2:% ( l
The total flight time T.,, only depends on the ion mass m and the magnitude of
the hyperbolic field applied to the reflectron. It is independent of the initial kinetic

energy of the ions.

For the situation of a time-of-flight mass spectrometer with a field-free
region, we have obtained a solution for the potential profile of the reflectron E(x)
by a numerical method rather than a mathematically derived equation as
illustrated by following discussion and Figure 3-2.

Assume that the ion with the lowest kinetic energy that has to be focused
has the kinetic energy V, in electron volts. The first grid of the reflectron is 0 V

and the next grid needs to be set at the voltage of V, in order to stop this ion.

 

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This second grid is set x, cm away from first grid. The velocity of this ion in the

field-free flight region and at the first grid position is

um = 12$
1 m ’

so the average speed of the ion in the region between the first reflectron grid
and the second reflectron grid is U”,/2. The total flight time of this ion in the field
free region as well as in the reflectron up to the turn around point x, is

2x
Tu=r,+r,=%+2U—1;— (3.12)
1 11 .

the factor 2 is added in second term because the ion travels both forward and
back backward through the reflectron.

Consider now a second ion with a kinetic energy V2=V,+dV (eV). This ion
will pass the second reflectron grid, a third reflectron grid needs to be introduced
and set at the voltage of V2 in order to stop the ion at that grid position. In order
to let the second isomass ion arrive at the detector at the same time as the first
ion, the distance between the second grid and the third grid must be set as x;
from the following calculation.

The velocity of the second ion at the field-free region and at the first grid

position is U,""’ = "21": .The velocity of the second ion at the second grid position

is U?) ="2% and the average velocity of the second ion after the first grid is

(U1‘2’ +U2’2’)/2 and after the second grid is ufl/z.

The flight time of the second ion at the turn around point is

 

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V,=V

lls ve

anda

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and a‘

81

L, 2x 2x
Tea—237217— “‘3’

so the value for x2 could be determined by solving

2 , 11‘”
x2 = [Trot - (1%‘1' 2 M2) :Uéz) )1 Z

 

(3.14)

This process can be continued for ions of a still higher energies,
increasing in increments of all. For the nth ion, which has a kinetic energy of
Vn=Vy+(n-1)dV,

lts velocity at the first grid position is

n) _ 1’;
U,‘ .."2 m (3.15)

and at the second gn’d position is

at") = "2(n-1)g’;—/- (3.16)

and at the 3rd to the nth grid positions is

 

U,"" =J2[(n-r)+1]-d;V-; i= 3,..., n (3.17)

So the distance between the nth and (n+1)th grids is

2 l n")
Xn=1Tu" “351'22 U’m) :wfl ”U; (3-18)

131

 

In this way the voltage and the position of each reflectron grid is defined. As the
energy increment dV is decreased and the number of grids and calculation steps

is thereby increased, a solution for the voltage profile that will provide nearly

82

perfect temporal focusing can be obtained. The calculated reflectron voltage
profile could be used to focus isomass ions of all m/z values.

Paul Vlasak modified the above calculation procedure for the design of a
reflectron for the TOF/TOF instrument. A constant increment for the distance
between each reflectron grid position was used for each calculation step and the
ion kinetic energy at each grid position was obtained. He also added a term in

the equation to allow consideration of the angle of ion entry.

3.2.2 Temporal focusing of isomass ions with the zero initial kinetic

energy, but different initial positions In the ion source.

For the segmented ring ion trap time-of-flight mass spectrometer. mass peak
broadening due to the range of initial ion kinetic energies is minimized by
applying a high voltage extraction pulse synchronized with the RF phase angle.
Ions at different positions in the segmented ring ion source gain different kinetic
energies during the ion extraction period. The reflectron can be regarded as a
device that temporally focuses isomass ions with an initial spatial distribution in
the ion source.

The essence of this temporal focusing is for all isomass ions to have the
same flight time between the application of the extraction pulse and their arrival
at the detector surface. The required profile for the reflectron voltage to achieve
this can be obtained by the numerical calculation method as described below
and illustrated in Figure 3-3. The ion extraction field normally consists of two

linear fields. As discussed in a later section of this chapter, the reflectron

 

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designed should be able to focus isomass ions with kinetic energies lower than
the actual minimum kinetic energy. So the ions initially in the acceleration field
region as well as in the extraction field region need to be temporally focused.
Assume that acceleration field has a distance of SA and an extraction voltage up
to VA, The lowest energy ion needs to be temporal focused is extracted at the
position S, with the extraction voltage of V, as shown in Figure 3-3. The second
ion is initially at the position of S1+dSA with an extraction voltage of V1+dVA. the
third ion is initially at the position of 31+2dSA with an extraction voltage of
Vi+2dV4. and the nth ion is initially at the position of S=Si+(n-1)dSA with the
extraction voltage of V=V1+(n-1)dVA. So the increments of the ion position and
the extraction energy in the acceleration region for each consecutive calculation

were dSA=SM(n- 1) and dVA=VA/(n- 1).

The velocity of the first ion in the field-free flight region is U,” = "21:71. The

flight time upon entering the field free region is 15%;}. The reflectron field
1

construction process is same as that described in the previous section. Since
first grid of the reflectron is 0 V, the next grid needs to be set at the voltage of V,
in order to stop this first ion. This second grid is set at the distance x, away from
first reflectron grid.

The velocity of the first ion in the field flight region and at the first grid

position is “951121;“ so the average speed of the first ion at the region

85

between grid one and grid two is U1”’/2. The total flight time of ion reaching the

 

detector is
28 L,, 2x
for U1“) U1") U1")

the factor 2 is added in third term because the ion travels both fonrvard and back

backward through the reflectron.

The velocity of the second ion in the field free region is U,""’ =112yn27’

where V., =V1 + W), is the kinetic energy of the second ion obtained from the ion

acceleration field. The flight time for the second ion to exit the acceleration

region is t, = -S‘U+2f—d/—824. The second ion with a kinetic energy V2=V,+dVA (eV) will
1

pass the second grid, a third grid needs to be set at the voltage V2 in order to
stop the ion right at that grid position. In order to let the second isomass ion
arrive at the detector at the same time as the first ion, the distance between the
second grid and the third grid must be set at the distance x: that is obtained from
following calculation.

The velocity of the second ion in the field free region and at the first grid

position is w2’="2‘7/n2-. The velocity of the second ion at the second grid

position is 142’="2-d—r‘;:4, its the average velocity after the first grid is

(U,‘”+U2(2’)/2, and after the second grid is Una/2.

The total flight time of the second ion is

 

86

 

+ dS L, 2x1+2x
”' U,‘2’ u?) 0:22 +1422 U?
50

S,+d$ L, 2x U“)
X2=[Tu- ( U(2)A2+U'—(-2)2+W2)]—i—

 

For the nth ion. the ion velocity in the field-free flight region is

11:") =,/2-‘%; v,.=v =v, +(n —1)dv,

and the flight time in the ion acceleration region is

S, _S, + (n-1)dS

‘= urn/2= urn/2

 

The velocity of the nth ion at the first reflectron grid position is

vi” = 2-V—"

m

at the second grid position is

 

,. dV
Ui ’ = 201-0774

and at the 3rd to the nth grid positions is

 

0;") =J2[(n-i)+1]-d—’:4-; i= 3... n

The total flight time for the nth ion is

8,-1- (n-1)d.’$2 2( 2x, +2x___,z_

I0
I n ‘II I" II nI—I—

 

 

The distance between the nth and (n+1)th grids is

(3.20)

(3.21)

(3.22)

(3.23)

(3.23)

(3.24)

(3.25)

(3.27)

87

 

 

_ 81 + (n -1)dSA L, " 2x, U,‘,”’
xn - {7.101 -[ U101) 2 + U‘M) +2 (Ul(n) + U131) )1} 4 (3'28)

After the ions extracted from the acceleration region are considered, the
construction of the reflectron voltage profile should be extended to focus ions
extracted from the source extraction region.

Assume the (n+1)th ion is initially located at the position of SA+dSs so the
extraction voltage is VM=VA+st, and the extraction field is ass/ave. The total

flight time of the (n+1)th ion in the ion acceleration and extraction region is

8 d3
1, = “in”, +AU1‘M’ 2 +-J$-,,:s,72 (3.29)

 

where the velocity at the exit position of acceleration field region is

U10”) = "2%; Vn+1=VA+st

and the velocity at the exit position of source extraction field region is

W
n+1=_s.
vi ‘lmz

The velocity of the (n+1)th ion in the field free region and at the first grid position

 

is
U1tn+fl = Eh (3.30)
m
at the second grid position is
14”” = J(st + (n- 2)dV, + V,)-2n-7- (3.31)

and at the 3rd to the nth grid positions are

88

 

=\flarv. +dVA(n-r)+ veg: e 3. n (3.32)

and at the (n+1)th grid position is

UL?"- _ {240” (3.33)
m

So the total flight time for the (n+1)th ion is

dSI S L,f
Tm = (n+1) 2 '1' (n+1) (n+1) 2 +—— (n+1) +
u, u, + U, U,

 

(3.34)

 

}£:(' 21x7 )+ x+1‘2
Ul(n+1) + Ul(+n1+1) u(n+1)

I-1 n+1
and the distance of added grid after the (n+1)th grid is

S L"
Xm1= {net-[W2+ u1n+1+ U(n+1) 2+—— U(n+1) ——+

2x, U2?"
gm...” + U,.,...)1}J—

 

(3.35)

 

For the (n+k)th ion, where k is the number to label the ions at the ion
source position SA+k2ng The total flight time in the source extraction region and

acceleration region is

 

8 d8 - k
= "£ka + U‘l‘ni-k) 2 TWZ (3'36)

The ion velocity at the exit position of acceleration field region is

up“ = 13%, v.,... =v + k - dv (3.37)

The velocity at the exit position of source extraction field region is

89

k'st
m

 

a?” = 2 (3.38)

The velocity of the (n+k)th ion at the first grid position is

U?“ =,’2YM (3.39)
m

and at the 2nd to the nth grid position is

 

U,"’*"’ =J(k- st+(n-i)dV,, +V,)%; i= 2,..., n (340)

and at the (n+1)th to the (n+k)th grid position is

 

Um") =J(k—j+1)d—;i2;j=1,...k ' (3-41)

The total flight time for the (n+k)th ion is

 

 

 

k - dS

Tm = W2 +
3-42

8,, L” ” " 2x, 2__x,,,,, ( )
ugmk) + U1(n+k) 2 +_U1(n+k)+ ’31 (Ul(n+k) + UI(+n1-I~lr))+ ngzk) _2
So the distance between the (n+k)th and the (n+k+ 1)th grid is

k - d8 8
X H: = {Tm ' [W + ”(n+“ +AU(n+k) 2 (3 43)
L 2x, U327,“ 2

 

+ k +"1"‘( k )1}
U‘(n+ ) U(n+ )+U(+n1+k)

The above calculation strategy gives a voltage profile for a reflectron that
is able to focus ions distributed initially at different positions in an ion source.
The variables in the above calculation are the parameters related to the ion
source (extraction field strengths, the dimensions of the two extraction field and

the starting position at the first extraction field), and the variables related to the

90

time-of-flight instrument constmction such as the length of the first linear field
region in the reflectron, the total length of the reflectron, and the length of the
field-free region. The voltage profile of the reflectron obtained from the above
calculation is applicable for isomass ions of all mlz values. A Mathcad program
has been constructed to calculate the voltage profile according to practical
instmmental parameters. Computer simulation (SIMION) has been used to assist
in the reflectron design and examine isomass ion temporal distributions at the

temporal focus position.

3.3. Computer slmulatlon end prectlcel design conslderatlon

The voltage profile obtained from the Mathcad calculation is a voltage profile
along the reflectron axial direction. lsomass ions with different kinetic energies
entering the reflectron will be near perfectly focused to the detector position with
a small temporal distribution. For a practical design, a stack of stainless steel
ring electrodes is used to achieve this reflectron voltage profile. A calculated ,
voltage profile that could be easily obtained in the real reflectron design is the
most desirable one.

The SIMION program for computer modeling of ion trajectories was used
to model the temporal focusing of several possible practical designs. The
computer simulation of the ion trajectories of a set of ions (m/z 100) initially
distributed in the ion source at various initial positions is shown in Figure 3-4. An
1800 V acceleration voltage is applied to the ion acceleration electrode. An

additional 800 V is applied across the ion source region. The total length of the

91

 

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field-free region before and after the front of the reflectron is 118 cm. The first
grid and the second grid of the reflectron are 2 cm apart. Twelve grids were
added after the second grid of the reflectron. The space between adjacent
reflectron grids is 1 cm. The voltage profile along ion axis of the reflectron is
shown in Figure 3-5. The lowest kinetic energy ion (1800 eV kinetic energy)
turns around at the second reflectron electrode. The ion distribution at the
temporal focus position is shown in Figure 3-4(b). From this figure we can see
that a temporal distribution of isomass ions (250 ns) still exists at the temporal
focus position. This is because the calculated voltage profile is not exactly
followed by the voltage profile generated between two adjacent reflectron
electrodes. Also the ion position deviation from the temporal focus position is
much larger for the ions with low kinetic energy than that for the ions with high
kinetic energy. This is partly because the relative energy distribution ratio is
larger for the low kinetic energy ions than for the high kinetic energy ions. More
significantly the low kinetic energy ions turn around at the reflectron position
closest to the second grid position. Severe field curvature exists in this region as
shown in Figure 3-5. From this observation, it is reasonable to expect that a
better temporal focusing could be obtained by using only the back part of the
reflectron. A voltage profile for such a design is shown in Figure 3-6; The ion
trajectory simulation for this profile is shown in Figure 3-7. In this design, the

lowest energy ions (1800 eV) turn around after the fourth reflectron electrode.

 

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An arrival time distribution (64 ns) still exists at the temporal focus position for
isomass ions but the magnitude of the deviation is decreased.

Using reflectron electrodes that are covered with mesh screens will give a
reflectron voltage profile along the reflectron axial direction that is close to the
calculated value. In a practical design, the more reflectron grids there are in the
ion flight path, the more ions will be lost due to the transmission efficiency of
these mesh screens. Much higher ion transmission would be obtained if fewer
mesh screens were used along the flight path. After the mesh screens from the
third reflectron electrode to the 11th reflectron electrode are removed. the ion
trajectory simulationchanges from that shown in Figure 3-7 to that shown in
Figure 3—8. The temporal focusing position moves 19 cm closer to the front of the
reflectron. A large temporal distribution (178 ns) and a increased radial
dispersion at the temporal focus position results. The equipotential contour of
the reflectron shown in Figure 3-8 is shown in Figure 3-9. The black lines
represent the reflectron electrodes. The red lines are equipotential contours with
the same voltages as applied to the corresponding electrodes. Since the
reflectron field along the axial reflectron direction after the second reflectron
electrode is not linear, the voltage profile distortions become more severe after
the removal of the mesh screens. The deviation from the derived voltage profile
changes the temporal focus position and the quality of the temporal focusing at

the temporal focus position for isomass ions with a broad distribution of kinetic

97

     

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The deviation of the voltage profile in the center of the reflectron
from the voltage profile applied to the reflectron electrodes creates

a distortion of the desired field and introduces an ion lensing effect.

 

99

energies. The lens effect caused by the curvature of the field lines spreads out
isomass ions in the radial direction.

These problems could be minimized by using the following two
approaches. First. we can readjust the reflectron electrode voltages manually
following the computer simulation to bring the voltage profile along the ion flight
path closer to the calculated values. In a practical situation, a reflectron quite
similar to the simulated reflectron (in three-dimensional scale) needs to be
constructed and then the electrode voltage values obtained from the simulation
adjustment could be applied to the real reflectron electrodes. For the reflectron
voltage profile shown in Figure 3-6, the reflectron field dramatically changes
before and after second reflectron grid. A dramatic voltage change will result in
severe field distortion in the vicinity of the mesh grid. A reflectron voltage profile
having a small field change in the vicinity of the second grid area is preferred.

The second approach is to adjust the reflectron design parameters to
obtain voltage profile such that a real voltage profile close to the calculated one
along the axial direction of the reflectron could be easily achieved by simply
applying the calculated voltages to the reflectron electrodes.

At this particular energy focusing situation (800 eV kinetic energy
distribution and 1800 V acceleration voltage, a voltage profile close to a linear
field as shown in Figure 3-10, was obtained through the Mathcad program
calculation by setting the total reflectron length to 50 cm. the total field-free

region distance (before and after the front the reflectron position) to 164 cm and

 

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the first linear field distance between the first reflectron electrode and second
reflectron electrode to 25 cm. An ion trajectory simulation of the time-of-flight
instrument with this reflectron configuration, and the applied voltage profile
shown in Figure 3-10 is shown in Figure 3-11. All the reflectron electrodes are
covered with mesh screens. The field between the first and the second reflectron
electrode is linear (In a practical construction situation, a series of reflectron
electrodes with voltage dividers will be needed to generate the linear field in this
region). An additional 25 electrodes. separated by 1 cm, are employed. The total
field-free region flight path before and after the reflectron is 176 cm. A small
isomass ion temporal distribution (11 ns) at the temporal focusing position and a
collimated ion beam are achieved using this reflectron configuration and this
voltage profile. After the mesh screens from the third reflectron electrode to the
26th reflectron electrode are removed, the ion trajectory simulation is shown in
Figure 3-12. A collimated ion beam and a small temporal isomass distribution
(24 ns) are maintained. This remains true even when only the first and last
electrodes are covered with mesh screen as shown in Figure 3-13. The
collimated ion trajectory beam and the small temporal distribution of isomass
ions (24 ns) at the temporal focusing position still exists. Considering that the
total flight time for an m/z 100 ion to reach the temporal focusing position is 51
,us. a resolution of 2000 (FWHM) will result if only the initial spatial distribution
broadening is considered. After some of the reflectron grids are removed as

shown in Figure 3-12 and Figure 3-13, the temporal focus positions only move

102

  

 

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1.7 cm and 3.3 cm further away from the front of the reflectron respectively. The
equipotential contours for the reflectron configurations shown in Figures 3-12, 3-
13 are shown in Figure 3-14. The electrodes are in black and the equipotential
contours are red lines. The voltage of each contour line is the same as the
voltage“ calculated and applied to the corresponding reflectron electrode.
Because the voltage profile is close to linear, these equipotential contour lines
are almost parallel and straight. These uniform contours provide the collimated
ion trajectory beams and the small isomass ion temporal distributions at the
temporal focusing position as they appear in Figures 3-12. 3-13.

A linear field voltage profile is applied to the same reflectron configuration
as shown in 3-15. The red line is the voltage profile obtained from the Mathcad
calculation. The black line is the linear voltage profile. The ion trajectory
simulation of the time-of-flight instrument with the reflectron that uses this linear
voltage profile is shown in Figure 3-16. A much larger isomass temporal
distribution at the temporal focus position (170 ns) results. The temporal
focusing obtained with the reflectron is quite sensitive to the voltage applied.
Small deviations from the calculated voltage profile results in a large temporal
distribution at the temporal focus position as shown in Figure 3-16. Increasing
the density of the reflectron electrodes generates voltage profiles close to the
calculated values along the axial reflectron direction.

The mesh screen that remains on the front reflectron electrode will cause

some field distortion near the grid aperture of the screen. However, since the

106

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Figure 3-16. Computer simulation of the ion trajectories (green lines) of mlz 100 ions initially at

different positions in the ion source.

The groups of red dots show the ion position at 0.5 ps flight time intervals.

The voltage profile applied to the reflectron is linear.

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109

ions enter the reflectron at their maximum speed, this field distortion effect will
has less effect than that of a grid separating areas of different field strength later

in the reflectron.

3.4. Conclusion

The theoretical considerations developed in Chapter Two formed a basis for the
design considerations of an actual segmented ring ion source. lsomass ions
extracted from the ion source can be temporally focused at the detector position
in a narrow ion bunch with a broad energy focusing reflectron. The reflectron
voltage profile can be obtained from a Mathcad program calculation based on
the strategy explained in this chapter. A reflectron with an appropriate length
and a reflectron field with near linear shape will be the most desirable. The
theoretical calculations and computer simulations of the reflectron design were
used to guide the practical design of the reflectron for the segmented ring,

storage time-of-flight mass spectrometer as discussed in the next chapter.

References:

 

1 Rockwood A. L.: An Improved Time-of-Flight Mass Spectrometer. Proceedings
of the 34th ASMS conference on mass spectrometry and allied topics, Cincinnati, Ohio,
June 8-13, 173-174 (1986)

2 a. Ji, Q., Vlasak, P. R., Beussman, D. J., and Enke, C. G.: A Reflectron for
Broad Energy Focusing of Ions. Proceedings of the 42nd ASMS Conference on Mass
Spectrometry and Allied Topics, Chicago, IL, May 29 - June 3, 1039 (1994)

 

Refit

Sov.

 

JETP

Time
Anal;

Aces.
37-43

89-11

LOllgi:
Proces

Slime
411-41:

110

 

b. Vlasak, Paul R., Beussman, Douglas J., Ii, Qinchung, and Enke, C. G.: A
Method for the Design of Broad Energy Range Focusing Reflectrons. Accepted, J. Am.
Soc. Mass. Spectrom. (1995).

3 a. Karataev, V. 1., Mamyrin, M. A. and Slunikk, D. V.: New Method Focusing
Ion Bunches in Time-of-Flight Mass Spectrometers. Sov. Phys. Tech. Phys., 16, 1177-
1179 (1972)

b. Mamyrin, B. A., Karataev, V. L, Shmikk, D. V., and Zagan V. A.: The Mass
Reflectron, a New N onmagnetic Time-of-Flight Mass Spectrometer with High Resolution.
Sov. Phys. JETP, 37, 1, 45-48 (1973)

c. Mamyrin, B. A., and Shmikk, D. V.: The linear Mass Reflectron. Sov. phys.
JETP 49, 5, (1979)

4 Ioanoviciu, D., Yefchak, G. E. and Enke, C. 6.: Second Order Space-Time
Transfer Matrix of the Two-Stage Electrostatic Mirror. Int. J. Mass Spectrom. Ion
Processes, 94, 281-291 (1989)

5 Boesl U., Grotemeyer J., Walter, K. and Schlag, E. W.: A High-Resolution
Time-of-Flight Mass Spectrometer with Laser Desorption and a Laser Ionization Source.
Analytical Instrumentation, 16, 1, 151-171 (1987)

6 Chen. C. C., and Su, C. S.: A Time-of-Flight Mass Spectrometer with an
Accelerating Field in the Reflecting System. Int. J. Mass Spectrom. Ion Processes, 124,
37-43 (1993)

7 Wollnik, H.: Time-of-Flight Mass Analyzer. Mass Spectrometer Reviews, 12,
89-114 (1993)

8 Kutscher, R., Grix, R., Li, G. and Wollik, H.: A Transversally and
Longitudinally Focusing Time-of-Flight Mass Spectrometer. Int. J. Mass Spectrom. Ion
Processes, 103, 117-128 (1993)

9 Gohl, w., Kutcher, R. Laue, H. J. and Wollnik, H.: A Time-of-Flight Mass
Spectrometer for Ions of Large Energy Spread. Int. J. Mass Spectrom. Ion Processes, 48,
411-414 (1983)

111

 

1° Grix, R., Kutscher, R., Li, G., Gruner, U., and Wollnik, H.: Rapid Comm. Mass
Spectrum, 2, 5, 83-85 (1988)

“ Cornish T. J. and Cotter R. J.: A Curved-Field Reflectron for Improved Energy
Focusing of Products in Tune-of-Flight Mass Spectrometry. Rapid Commun. Mass

Spectrum, 7, 1037-1040 (1993)
'2 Makarov, A. A., Raptakis, E. N., and Denick P. J.: Pitfall on the Road to the

Ideal Tum-of-Flight Mirror: Ideal Time Focusing in the Second Stage of Tandem Mass
Spectrometers. Int. J. Mass Spectrom. Ion Processes, 146/147, 165-182 (1995)

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Chapter 4 Design and construction of a segmented rlng, ion trap

storage source/reflectronltime-of-flight mass spectrometer

4.1 Background

The design and construction of the reflectron time-of-flight mass spectrometer
with a segmented ring, ion trap storage source started late in the summer of
1993. The vacuum system with electronic feedthroughs and mechanical motion
feedthroughs, the mechanical parts of the reflectron, and the parts of the
detector and the source were mainly fabricated in the machine shops at
Michigan State University before the summer of 1994. The modifications of the
reflectron, the source and detector elements were completed with the help of the
machine shops at the University of New Mexico. The static voltage supplies to
the reflectron electrodes, the detector, and the ion source were constructed at
the University of New Mexico during the fall semester, 1994. Beginning in spring,
1995, Michael Davenport helped with the design and constmction of the dynamic
voltage supplies for the segmented ring ion storage source which is critical to
the success of this project. In a later experimental stage of this project, Eric
Hemenway helped convert the Labwindows CVl (program of the TOF/T OF
instrument for data acquisition using a LeCroy oscilloscope. Dr. Yefchak and
Hewlett Packard Inc. provided the data acquisition board with software for the

continuous spectrum acquisition. Dr. Overney wrote a data processing program,

112

tit

113

which uses a peak finding technique for noise reduction, and which provides the

capability to obtain reconstructed ion chromatograms.

4.2 Design and construction of the time-of-flight mass spectrometer

4.2. 1. Instrument overview

The reflectron time-of-flight mass spectrometer with a segmented ring, ion trap
storage source is shown in Figure 4-1. An HP 5890 gas chromatograph is used
for sample introduction. During the ion storage period, an RF voltage is applied
to the segmented ring electrode and both end caps are grounded. Ions
generated by electron impact ionization are stored in the segmented ring ion
storage source. During the ion extraction period, high voltages are applied to the
rear end cap and ring electrode elements. An electronic circuit was specially
designed for this instrument for fast switching between the extraction voltage
and the RF voltage. The timing circuit designed for this instrument is able to
synchronize the extraction pulse with the RF phase as well as the trigger for the
transient recording of the spectra. A broad kinetic energy focusing reflectron was
constructed to give a small temporal distribution of isomass packets at the
detector position. Ten-turn pots are used for the adjustment of the voltages for
different instrument parts and the control of the timing system. Computer-
controlled data acquisition is achieved by using a Gateway P5-90 computer
interfaced to a Precision Instrument Transient Recorder board or a LeCroy

oscilloscope with GPIB board, The instrument is intended to demonstrate the

114

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advantages of using the segmented ring ion trap source for time-of-flight mass
spectrometry or the time-of—flight mass analysis of ions generated in the
segmented ring ion storage trap. These advantages are fast spectral generation
rate, good mass resolution, very high sample utilization efficiency, and wide

dynamic range.

4.2.2 Vacuum system

The details of the vacuum system for the time-of-flight mass spectrometer are
shown in Figure 4-2. The source chamber is a fourway cross made of a 6 inch
inner diameter stainless steel tube. Six half nipples with 1 inch inner diameter
are located on both sides of the cross. They are designed to be used as ports
for sample introduction, vacuum gauge mounting, and RF electronic feedthrough
mounting. A glass viewport is mounted on the top flange of the cross. One side
flange is for the source and electronic feedthrough mounting and another side
flange was modified for the attachment of the flight chamber. The bottom port is
attached to one turbo molecular pump through a ISO/ CF converter. The flight
tube is a 58 inch long stainless steel tube with a 10 inch diameter. A 5 inch inner
diameter half nipple is welded to the one side of the flight tube (7 inches away
from the source side flange) for the attachment of the detector mounting flange.
A 6 inch inner diameter half nipple is welded to the bottom of the flight tube (20
inches away from the source side flange) for the attachment of the other turbo
pump. One end of the flight tube is attached to the source chamber and the

other end is for the attachment of the reflectron mounting flange. A baffle is

 

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117

placed between the fourway cross source chamber and the flight tube chamber.
An 8 inch long stainless steel tube of 1 inch inner diameter passes through the
baffle. This allows ion transmission between the source chamber and the flight
tube while limiting the vacuum conductance to allow the differential pumping.
Two 1 inch inner diameter half nipples are attached to this flight tube for
mounting a vacuum gauge and an electronic feedthrough.

Two Leybold Trivac 08A rotary vane pumps are used as rough pumps.
Two Balzers TPH 520 turbomolecular pumps are attached to the source
chamber and flight tube respectively. An oil filter and a butterfly valve are
attached to the transfer line between the rough pump and the turbomolecular
pump to prevent back streaming of the pump oil. Two Granville-Phillips GP 270
ion gauge controllers are used to monitor the pressures in the rough vacuum

and high vacuum region.

4.2.3 Sample introduction

Samples were introduced through a glass capillary column contained in a heated
transfer line (Finnigan MAT, San Jose, CA) and emanating from a Hewlett-
Packard Model 5890 chromatograph. Samples were either introduced
continuously from a helium-swept vial contained in the chromatograph oven, or
by injection through the chromatograph’s injection port. For steady-state sample
introduction, the sample introduction rate is controlled by using a guard column

of different inner diameters or by adjusting the GC oven temperatures.

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4.2.4 Field free flight region voltage

A 7 inch inner diameter cylinder made of stainless steel mesh that is 50 inch
long is placed in the flight tube. It is electrically isolated from the vacuum
chamber by attaching ceramic spacers to it. A voltage of -1800 V (maximum up
to - 2500 V) is applied to this mesh to provided a field free flight region voltage.
This configuration allows the DC and RF voltages applied to the segmented ring
ion trap source to be referenced to the ground potential. The relatively low
voltages required in the source region, because of the floating flight path, avoids
electric discharge when the ion source is operated at the higher pressures that
occur with chromatographic introduction of the sample. Unfortunately,
introduction of the stainless steel mesh introduces a large surface area which

increases the time required to reach a low pressure in the vacuum chamber.

4.2.5 Segmented ring ion storage source with electron impact ionization

The design and construction of the segmented ring, ion trap storage source is
based on the computer simulation results described in Chapter Two. A detailed
drawing of the electrodes used in the source assembly is shown in Figure 4-3(a).
A representative diagram of the ion source with electron impact ionization
capability and ion acceleration electrodes is shown in Figure 4-3 (b). The
distance between the exit and rear end cap is 9.4 mm. These two elements are
covered with 86% transmission mesh screens. The ring electrode elements are
2.5 mm apart. An additional three electrodes are placed after the exit end cap

with 0.15 inch ceramic spacers between them, three electrodes and the exit end

119

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cap are electrically connected to a voltage divider made up of three 2M0
resistors, this divider provides a linear ion acceleration field. The last
acceleration electrode is also covered with a mesh screen. Two electron entry
electrodes located above and below the segmented ring ion trap source provide
two 1x10 mm2 slits to guide the electron beam into the ion source. Two filaments
are located above and below the two entry slits. The two electron shielding
electrodes are designed to help guide electrons into the ion source and reduce
ion generation outside of the ion source.

In order to obtain a uniform extraction field, the source elements were
designed (as shown in Figure 4-3(a)) to have 0.01 inch, 0.02 inch and 0.03 inch
increasing thickness from the inner diameter to the outer diameter. The
computer simulated extraction field of this unique ion source design is shown in
Figure 4-4. The voltages across the acceleration electrodes are -600 V, -1200 V,
and -1800 V. The voltages applied to the exit end cap, the two ring electrode
elements, and the rear end cap are 0 V, 200 V, 500 V, and 700 V. The voltages
applied to the electron entry electrode, the filament and the electron shield
electrodes are 0 V,-25 V, and -50 V. The red lines are equipotential contours
from 50 to 650 V in 100 V increments. The important advantage of this source
design is that the uniform, linear extraction field remains essentially undistorted
by the filament electrode elements of the electron impact ionization source.
During the ion storage period, an RF voltage is applied to the ring electrode

elements. The computer simulated electron trajectories at ring electrode

121

 

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period. The voltages across the acceleration electrodes are -600 V,

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elements, and the rear end cap are 0 V, 200 V, 500 V, 700 V. The voltages
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voltages of 0 V, -300 V, and 300 V are shown in Figure 4-5. The green lines are
trajectories. The electrodes are shown in black and the voltages applied to them
are the same as described in Figure 4-4, except for the voltage applied to the
ring electrode. When the RF is at 0 V, electrons enter the ion source and spread
over almost the entire source region. When the RF voltage is at -300 V, the
electrons don’t have enough kinetic energy to get into the ion source. When the
RF voltage is at 300 V, electrons are pulled through the ion source by the
internal field. The electron trajectories are quite sensitive to the configuration of
these related electrodes and the voltages applied to them.

The components such as the electron entry electrode, the filament and
the electron shield were made and assembled by myself and are not accurately
machined. Each time they are taken apart and assembled again, the relative
position of these electrodes shifts slightly. The overall behavior of the source is
quite reproducible although the optimized bias voltage applied to the filament is
not exactly the same each time. Another concern is that electrons get into the
ion source only during the positive half of the RF cycle. However, this need not
affect the ionization efficiency significantly because the sample introduced
during the negative half of the RF cycle, considering the diffusion velocity of
molecules, will be still in the ion source when the RF changes to the positive half
cycle. Although ionization does not occur throughout the whole RF cycle,

molecules introduced over the whole RF cycle can be ionized.

123

 

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4.2.6 Elnzel lens and deflectlon plate

A detailed drawing of the Einzel lens is shown in Figure 4-6. Three cylindrical
stainless steel lens elements are separated by two 0.05 inch ceramic spacers.
The inside diameter of these lens elements is 0.62 inches. The length of the lens
elements on both sides are 1 inch and that of the center lens element is 0.5
inches. Computer simulation of the ion beam focusing is shown in Figure 4-7. A
diverging beam with 1800 eV kinetic energy is collimated by this lens. The lens
voltages applied are 0 V, -1800 V, and 0 V respectively. The focal length of the
Einzel lens depends on the lens voltages applied and the kinetic energy of the
ion beam passing through it. The simulation shown in Figure 4-7 is an ideal
case. In a practical situation, the distribution of ion kinetic energies and the
radial distribution away from the lens axis will result in both a chromatic
aberration (due to different kinetic energies) and a coma effect (due to initial
positional deviation from the axis). On the other hand, the degree of ion
dispersion depends on the geometry of the ion source. With the unique design
of the segmented ring ion trap, a uniform extraction field is generated. So the
dispersion velocity perpendicular to the flight axis is mainly due to the random
thermal motion and the RF trapping field. Compared with the high velocity in the
direction along the ion flight path axis, the resultant degree of dispersion is very
small.

An ion deflection electrode assembly that consists of two stainless steel

plates is located after the Einzel lens electrodes. One of the stainless steel

125

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plates is a 3 inch long and a 3/4 inch wide. It is connected with a voltage near
the field free flight voltage to steer ions in a correct direction in the flight path.
The other is 3 inches long and 1/2 inch wide. It is connected with a voltage (400
V to 800V) higher than the field free region voltage during the ionization period
(to block ions into the field free flight chamber) and at the field free region
voltage during the ion extraction period (to allow ions into the field free flight
chamber). A computer simulation of the ion trajectories of these two situations is
shown in Figure 4-8. During the ionization period ( Figure 4-8 (a)), one plate has
a more positive voltage than the field free voltage as shown in the figure. The
red lines represent the equipotential contours from -1200 V to -1800 V at 50 V
increments. The green lines are ion trajectories of ions with 1800 eV kinetic
energy. They are deflected as they pass the deflection plates. During the ion
extraction period (Figure 4-8 (b)), all of the electrodes have the field free voltage

and the ions pass without deflection.

4.2. 7 Bread energy range focusing reflectron

Based on the developmental method discussed in Chapter Three for a broad
energy range focusing reflectron design, a reflectron as long as 50 cm needs to
be constructed and a nearly linear reflectron voltage profile should be applied to
the reflectron electrodes to give a good temporal focusing of isomass ions with
broad kinetic energy distribution. Our present system prevents the
implementation of this design concept; the two motion feedthroughs attached to

one 10 inch CF flange are not strong enough to support the weight of so many

128

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reflectron electrodes. The actual reflectron design is shown in Figure 4-9. Each
reflectron electrode is a stainless steel ring that has a 4.5 inch outer diameter, a
3 inch inner diameter and a thickness of 0.03 inches. The first and the second
reflectron grids are reflectron electrodes covered with 86% transmission mesh
screens. A linear field is formed by applying the voltages to these two reflectron
grids and connecting the electrodes between them with 3 M9 resistors in series.
The rest of the electrodes are provided with adjustable voltages from another 20
electrical feedthroughs. A detailed description of the electronic voltage
adjustment for this reflectron is described in a later section. All the reflectron
electrodes and grids are separated with ceramic spacers with a thickness
varying from 0.382 to 0.385 inches purchased from Newark Electronics. Two
motion feedthroughs mounted on one end flange and a stainless steel rod (0.25
inch diameter) mounted to that flange provide mechanical support and
directional adjustment of the reflectron to steer the ion beam to the detector
surface. The electron voltages applied to the reflectron electrodes are first
calculated from the Mathcad program described in Chapter Three. Because the
length of the spacers is not an integer unit, an accurate computer simulation and
an iterative adjustment from the computer simulation are not possible. A manual
tuning of the 21 pots which control the reflectron electrode voltages was used to
obtain the best resolution. The Mathcad program calculation and computer

simulation , however, provided a good “first approximation" for this adjustment.

130

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4.2.8 Detector

A “Chevron assembly” detector using two 40 mm diameter MCP plates is shown
in Figure 4-10 (a). The anode is a 0.03 inch thickness, 2.75 inch outer diameter
gold plated stainless steel plate. The ion entry electrode was covered with a
86% transmission mesh screen so the electric field in the field free region will
not be distorted by the voltages applied to the detector electrodes. A detailed
drawing of the detector ring electrodes are shown in Figure 4-10(b). They are
stainless steel rings of 0.03 inch thickness, 1.75 inch inside diameter and 2.75
outer diameter. These rings were made as flat as possible to keep good contact

between the ring electrodes and MCP plates.

4.2.9 Electronic control system for the tlme-of-flight mass spectrometer

4.2.9.1 Static voltage supply

The schematic of the static voltage supplies for the field free region voltage,
detector voltage, and lens voltages is shown in Figure 4-11. A Bertan -2 kV
adjustable power supply is used to provide the field free flight path voltage, Two
Acopian power supplies (200 V and -200 V) are referenced to this voltage. Four
ten-tum pots of 100 kg in parallel are connected to the positive and negative
output of these two power supplies to give the 400 V variation over the shielding
potential for the lens electrodes and ion deflection electrodes. Another four

adjustable high voltage power supplies of -300 V, -1.5 W, -2.5 kV and -5 W are

132

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Einzel lens, and the detector

134

used to provide the voltages for the three ring electrodes and the middle Einzel
lens electrode.

The schematic of the voltage control for reflectron electrodes is shown in
Figure 4-12. A positive 1.5 kV and a negative 1.5 kV power supply provide the
high and low reference voltages for the reflectron. Twenty-one 10 turn pots (50
k0) are connected in series with these two power supplies. These twenty one
pots are used to set and tune the reflectron electrodes starting from the second
reflectron grid as shown in Figure 4-9. These reflectron voltages are manually

monitored by using a KEITHLEY 195 high precision digital multimeter.

4.2.9.2 Dynamic voltage supply and timing control system

The electronic system for generating the RF voltage and the extraction
voltage for segmented ring source electrodes shown in Figure 4-13 was
designed and constructed with the help of Michael Davenport. To obtain the
highest resolution and intensity from the storage/extraction cycle, it is important
to find the best phase of RF (storage) cycle in which to initiate the extraction
cycle and to maintain this ideal phase relationship for all experiments. This ideal
timing for the SRS-TOF mass spectrometer begins with a common timebase
(Wavetek Function Generator, model 171) to drive the RF amplifier and the
extraction timing. The TTL signal from the function generator is routed through
an adjustable delay to provide the optimum phase for all subsequent timing
functions. This delayed clock is connected to a programmable modulus counter

to generate an extraction clock signal with a frequency 1/128 to 1/16384 that of

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the RF frequency. The extraction clock signal triggers an ionization timer,
enabling electrons to enter the trap for an adjustable time from 6 usec to 600
usec. The end of the ionization time triggers the extraction delay timer with a
range from 8 psec to 1000 usec. The end of this ion storage time triggers the ion
extraction pulse generator. To preserve the desired RF phase/extraction timing
relationship, the extraction trigger is synchronized with the delayed TTL clock
signal by a H074 D latch. The typical extraction trigger pulse width is 2p sec.
The synchronized extraction trigger is buffered and routed to the data acquisition
system, detector display, and high speed HV switches attached to the electrode
elements of the segmented ring. Prior to the extraction trigger, a 1.2 MHz, RF
signal adjustable from 200 Vpp to 900 Vpp is applied to the segmented ring of
the ion trap through a high speed, high voltage N-channel MOSFET assembly.
At the command of the extraction trigger pulse, the RF side is turned off and the
extraction voltage FETs are turned on for the duration of the extraction pulse. At
the falling edge of the extraction trigger, the extraction voltage MOSFET
switches are turned off and the RF side is turned back on. All switch operation is
break-before—make. Extraction voltages for the ring discs are supplied by
individual 10-1200 V Spellman MP power supplies. The RF is generated with a
high speed, high power APEX PA09 op amp and the Hi-Q RF head from an

Barty model Extrel quadrupole power supply.

138

4.2. 10 Data acquisition of the time-of-flight mass spectrometer

After each high extraction voltage pulse is applied to the ion source, the arrival
times of the isomass ion packets to the detector and the voltage response of the
anode current over a 50 Q terminator are recorded as a single mass spectrum
transient. Since the time-of-flight instrument can give several thousand
extractions per second, the spectral generation rate is limited by the speed of
data acquisition. The speed of the data acquisition is mainly depended on the
transient recorder characteristics such as the acquisition time of the each data
point, the time for each transient summation, and the data transfer time of every
set of summed mass spectra to the data storage device. The summing rate is
inversely proportional to the number of the data points to be acquired in each
transient. In order to get a good quality spectrum, a certain amount of data
points is required. Another important characteristic of the transient recorder is
the resolution of the signal intensity. This directly affects the signal to noise ratio

obtained when the signal intensity is extremely low.

4.2.10.1 Data acquisition with the LeCroy oscilloscope and GPIB board

The LeCroy 9450 digital oscilloscope interfaced to a P5-90 computer by a GPIB
board is used for data acquisition during the initial period of the experimentation.
A Labwindows/CVI program written in C language is used to obtain the spectrum
data from the oscilloscope.

The LeCroy 9450 digital oscilloscope provides the true summed average,

450 megasamples per second for each transient and 10 bit analog to digital

139

conversion resolution for the signal intensity. This data acquisition setup is
mostly used to record spectra when steady state sample introduction is used.
The mass spectral peak area is calculated from the ASCII file obtained by using

a commercial application program called ORIGIN.

4.2.10.2 Data acquisition with the Precision Instruments Tramient Recorder board

A Precision Instruments model 9825 transient recorder located in a Gateway
2000 P5-90 computer was provided by Hewlett Packard. Software written by Dr.
George Yefchak is used to obtain the spectrum transient data when using this
transient recorder. The Precision Instruments model 9825 transient recorder
provides 200 megasample data points per second for each transient and 8 bit
analog to digital conversion resolution for the signal intensity. The data storage
time for each summed transient spectrum is 16 ms if each spectmm has 16 k
data points. The maximum signal input voltage for the Precision Instruments
could be up to 1V. This data acquisition setup is used to evaluate the detection
limit and dynamic range of this instmment. The data file obtained is in DPl
format. Dr. Gregor Overney wrote a C program to convert a set of consecutive
mass spectra, which is acquired in one sample injection, into a reconstructed
ion chromatogram (RIC) for that injection. A peak finding technique is used in
this RIC program to reduce background electrical noise. Two parameters ( peak
width and threshold ) are input for maximum accuracy in peak detection.

The performance and its advantages as a detector for gas chromatograph

of this segmented ring, ion trap storage/reflectron/time-of-flight mass

140

spectrometer were evaluated. The experiments performed and the results

obtained are discussed in the following chapter.

Chapter 5 Characterization of the segmented ring ion trap

source/retlectron/time—of-flight mass spectrometer

5.1 Introduction

The performance of the SRS/TOF mass spectrometer was evaluated with regard
to mass resolution, mass range, linear response and detection limit for GO
introduced analytes. Ion storage capability was demonstrated using several
compounds. Time-of-flight mass analysis was used to determine the m/z values
and the abundances of the ions present in the trap at the time of extraction. The
controlled parameters were the ionization conditions (filament offset relative to
the rear cap electrodes and filament current, the ionization time, the RF voltage,

and the delay time between the cessation of ionization and ion extraction.

5.2 Mass resolvlng power of the SRS/TOF mass spectrometer

One measure of the merit of time-of-flight mass analysis is the resolution
obtainable over the mass range being measured. For time-array detection,
adequate resolution must be obtained over the entire mass range populating
each extraction. In this study, the resolution is determined by the uniformity of
the extraction field, the magnitude of the extraction and accelerating fields, the
phase relationship between the extraction field and the RF field, and the energy
focusing ability of the ion reflectron and the total flight path. The mass spectrum

of PFTBA obtained with this system is shown in Figure 5-1. The RF voltage

141

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143

applied is 800 V. Three regions of the mass spectrum are expanded to show the
mass resolution obtained in each area. In every instance, the resolution
achieves or exweds that necessary for unit resolution.

Further improvement of the mass resolving power could be obtained by
constructing a reflectron that has a reflectron voltage profile close to the
theoretical profile as discussed in chapter three. As proposed in the competitive
grant renewal proposal submitted on November, 1995 for this project, a
reflectron with a calculated voltage without steep field change will give much
higher resolution. A more accurate and closer spacing between electrodes as
well as accurate voltage settings for each reflectron electrode will also improve

mass resolution.

5.2. 1 7779 eflbct of RF phase at the time of ion exhaction on mass resolution

At the time of ion extraction, the RF voltage is turned off and the extraction pulse
is applied. The effect of the phase of the RF field at the time of extraction on the
sensitivity and resolution of the TOF analyzer was studied. Ideally, the extraction
pulse should be applied to the ion source when the ions are at their minimum
kinetic energy. As discussed in chapter 4, electrons pass through the ion source
with a maximum density and kinetic energy at an RF phase angle of 90°
(sinusoidal wave). It is expected that most ions are generated in this RF phase
region. As discussed in Chapter 2, ions generated at the 90° RF phase angle will
have a minimum kinetic energy at RF phases 90° and 270°. Ion extraction
applied at these two RF phases should give the best resolution. The relationship

of the extraction pulse with the phase angle of the RF voltage applied to the two

 

144

ring electrode elements and the rear end cap of the ion source is shown in
Figure 5-2. The effects of the phase angle of the extraction on the mass spectra
of PFTBA are shown in Table 5-1. The data in this table clearly document the
importance of the moment of extraction relative to the phase of the RF field.
Considen'ng only the effect of field-induced acceleration on the ions during a
single RF cycle, at the phase angle of 270°(a), ions are at their lowest kinetic
energy and the direction of the RF voltage change is same as the direction of
the extraction voltage change. This gives the best mass resolution and greatest
peak intensity as shown in Table 1.

At the 0° moment (b), the ions are at their maximum acceleration away
from the center of the ion source at the time of extraction voltages are applied.
Because the direction of the extraction voltage change is the same as the
direction of change of the RF voltage, this gives the second best resolution and
intensity. At the 90° phase, the ions are also assumed to be at a minimum kinetic
energy. The direction of change of the extraction field at this RF phase angle is
opposite to the direction of RF field change. As a result, significant delay period
exists between the 90° phase angle and the rise time of the pulse as shown in
Figure 5—2(c). It is quite possible that Ions are initially scattered by the opposite
directions of the extraction and RF fields. Both the sensitivity and resolution are

diminished at this phase angle. At the 180° position(d), the ions are at their

 

Voltage

 

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145

,_ -_ Ring electrode element
(a) 270 degree 1 HM Ring electrode element
Rear end cap

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r \, ’,
I \ I f

 

 

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i
4/I’A/J
’/ l
k... I
r

(0)90 degree F _  l

 

800i

400

400

 

 

 

Time (microsecond)

Figure 5-2. Synchronization of the extraction pulse with RF phase
at RF phases of (a)270°, (b)0°, (c)90° and (d)180°.

146

TABLE 5-1

Effects of the timing of the extraction pulse in relation to the RF phase

 

 

 

 

 

 

 

m/z 69 m/z 131 m/z 219
RF Phase height/ resolution height / resolution height/ resolution
270° 40,489 / 756 16,702 / 857 11,353 / 1019
0° 41,510 / 663 16,760 / 772 11,41 6 / 986
90° 15,370 / 541 4,815 / 562 2,936 / 767
160° 5,394 / 359 1,995 I412 1,376/ 645

 

 

 

 

 

147

highest energy position moving away from ion trap center and along the
extraction axis, but the direction of extraction voltage is opposite to the direction
of RF voltage change. Again the resolution and sensitivity are both greatly
reduced. The significant loss in peak height and resolution at these latter two
phase angles means many of the trapped ions are not effectively extracted.

For all of the phase angles studied, the direction of ion motion in the
trapping field appears to have little effect on the quality of the resulting TOF
analyses. It also appears not to be the kinetic energy of the ions when the
extraction pulse is applied but rather the direction of the field changes upon
application of the extraction that most affects the quality of the mass spectrum.
Regarding the advantageous cases, the similarity of the results at 270°and 0°
suggests that optimum performance may be achieved with a considerable

leeway along the phase axis from 270 to 0°.

5.2.2 The effect of the electron bias voltage on mass resolution

For the conventional quadrupole ion trap with electron impact ionization, the
trajectories of the electrons are effected greatly by the RF voltage‘. For the
segmented ring ion trap source, the electron trajectories are quite responsive to
the electronic configuration of the source assembly and RF voltage. Because
some parts of the ion source assembly such as the filament assembly and the
electron shield electrodes were not accurately machined, the relative positions
of the electrodes are not exactly the same after cleaning and reassembly and

the optimum bias voltage will change. However, the overall performance of the

 

148

instrument is essentially unchanged. The effect of the bias voltage on the
observed trapped ions was investigated using chlorobenzene as the analyte.
The peak heights of the major ions in the spectrum as a function of the voltage
difference between the filament and the electron entry electrode are shown in
Figure 5-3(a). The RF voltage applied is 600 V”. In the ion trap, the filament
bias voltage is not a direct measure of the ionizing electron energy because of
the large effect of the RF field on the electron trajectories. However, the filament
bias voltage is a measure of the energy the electrons possess when first
encountering the RF field and it is reasonable to assume that the more energy
the electrons have at this point, the more energy, on the average, the electrons
will possess throughout their trap excursions. The initial slope of this response is
similar to that observed for other types of mass spectrometers where sufficient
energy for effective ionization must be present. The maximum is reached at
lower applied energies than with other sources, undoubtedly due to the
accelerative effects of the RF fields. The negative slope at the higher energies is
interesting since the trap should not lose these ions. When the peak areas are
plotted, as in Figure 5-3(b), the apparent decrease in abundance at the higher
filament bias voltages largely disappears. This is an indication that, at higher
bias voltages, it is the temporal focus at the detector that is suffering, not the ion

abundance.

149

 

 

 

 

:3113 E ;::::::\
*- ‘.\“\
.0 E : -;*
2 r . \35- mlz 112
a) ...- . \-*’T-\‘\‘
E 0 5 - ., "-
E 3 .1 (a) mlz 77
<6 :
(D _
0- ;
o 20 40 60
30 *' ,/‘\.\ ml Z 1 12
/ K
9 *4/\ ...::::::::“—c
(D _ A/ P/ - \_____
S 20 _ ,/ I“, Z 77
8 d’
:3 ' (b)
4‘ 10 _
CU .
a: _
0- .
o 20 40 60

Bias voltage of filament (V)

Figure 5-3. The effect of filament bias voltage on the peak
height (a) and the peak area (b) of the major ions of
chlorobenzene

 

150

5.3 Characterlzatlon of Ion storage of the segmented rlng lon trap

5.3. 1 Ion loss for the normal electron Impact Ion source for the time-of-

fllght mass spectrometer

For the normal ion source for the time-of-flight mass spectrometer, the potential
well generated by electron beam may store a small portion of ions generated.
Most of ions will leave the ion source due to ion charge repulsion and thermal
ion motion. Without an RF voltage applied, acetone was introduced into the ion
source chamber. The pressure in the source chamber was 9x10‘7 torr. The peak
area of the mlz 43 ions was obtained for different delay times between the
cessation of ionization and the start of ion extraction as shown in Figure 5-4.
More than 80% of the ions leave the ion source after 4.7 us. This demonstrates
the importance of ion storage between extractions for making a significant

improvement in the ion utilization efficiency of TOF mass spectrometry.

5.3.2 Storage mass range with the RF voltage

The mlz range over which ions will be efficiently trapped is dependent on the
frequency and amplitude of the RF voltage as well as the dimensions of the ion
trapz. The expected relationship is shown in equation(1) which is derived from
the Mathieu equations of motion in the trap. Since no DC voltage is applied, only

the function for qz need be considered.

00000.08 00. 000 00000.00. .0 00000000 0003.00
0.0.10.0... 00. .0> 000.000 .0 00. mv 0.0. .0 00.0 .000 0.; Tm 0.30.“.

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0. m o v N O

 

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151

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.T

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152

77; =( qz IZeVerz) (equation 1)

The terms in equation 1 are: m/z = mass to charge ratio, V= RF voltage (peak to
peak), 0 a RF frequency, r = the ring electrode radius and e is the electron
charge.

This relationship was studied in our system by observing changes in the
spectrum of PFT BA as a function of the RF voltage as shown in Figure 5-5(a-f).
In these experiments, the dimensions of the source and the RF frequency were
invariant. An estimate of the value of qz at the low mass cutoff was obtained by
observing the beginning of attenuation of mlz 69 at V = 800V. From equation 1,
a boundary value of qz for the low mass cutoff was calculated to be about -0.84.
The high mass cut-off for zero DC voltage is not predicted by the theoretical
stability diagram; rather it is caused by decreasing depth of the potential well as
qzdecreases below ~—0.7 as mlz increases. In the current segmented n'ng ion
trap storage source, the practical high-mass limit is between 7 and 8 times the
low-mass cutoff. The use of ion cooling in normal ion trap mass spectrometers
results in a larger mass range for these devices. However, the mass entrapment
range of the segmented ring trap is sufficient without cooling for most gas
chromatographic applications.

An attempt to increase the storage mass range was made by adding a
small DC offset to the end cap electrodes of the ion storage source. Although the

stability diagram obtained by computer simulation of the segmented ring ion trap

153

 

 

 

 

 

 

 

 

 

 

 

: Vrf=500 v
: 1 (a)
i - L i .. 5 -1-
(b)
Vrf=600 v
z = l
P [.1 L..--J-_.L.-_-__--MW

 

 

A A

 

Peak intensity
i

(d) Vrf=800 v

(f) Vrf=1000 v

E (e) Vrf=900 v

 

 

b 260 400 600
mlz

Figure 5-5. Mass spectra of PFT BA taken with various RF voltages
on the ion trap. As the RF voltage is increased, increases in both
low mass and high mass cutoff occur.

 

154

as discussed in Chapter 2 indicates that the maximum mass range would be
achieved at zero DC offset, in the quadrupole ion trap, the actual maximum
storage mass range is often obtained when a small degree of DC offset is
applied. The ion storage mass range is examined with a DC offset voltage
applied from -3 V to +3 V. The representative mass spectra of PFTBA are shown
in Figure 5-6. There is almost no effect when a DC +3V offset voltage is applied.
When -3V is applied, m/z 502 peak, which existed in the zero offset or +3 V
offset conditions disappears. This indicates that there is no significant space
charge or RF demodulation contribution to the field sensed by ions.

Although no significant improvement was achieved by applying a DC
offset, we believe a still wider mass range can be obtained by optimization of the
physical dimensions and electrical parameters, or, if necessary, by switching
between values of V., to obtain low and high mass ends of the spectrum
alternately. Additionally, further improvements in the ion storage capacity and
mass range may be achieved by changes in the SRS geometry and electronic
control. Experiments of different radial to axial dimension ratios, RF frequency
and voltage could make significant improvements as demonstrated in the history
of the development of the quadrupole ion trap. As proposed in the competitive
grant renewal of this project, more segmented ring elements could be used to

form a field closer to the optimum ion storage field.

 

20000

1 0000

20000

1 0000

Peak Intensity

20000

1 0000

f?

 

155

 

 

 

 

 

 

 

 

 

 

 

 

 

 

’ No DC Offset

* w (a)

r --lll It 111. L - - L L

0 100 200 300 400 500 600

mlz

— I DC Offset -3 V

L (b)

r . in .1 1111 L - e 0

O 100 200 300 400 500 600
mlz

[ DC Offset 3V

r

-_ (c)

r: - 11‘ H 1 11 L - - J. .

0 1 00 200 300 400 500 600
mlz

Figure 5-6. The effect of DC offset on the ion storage mass range.

156

5.3.3 Ion buildup and Ian storage of the segmented rlng Ion source

The trapping characteristics of the segmented ring ion source were documented
in a series of experiments designed to reveal the nature of the ion accumulation
during the ionization part of the cycle. A sample vial of chlorobenzene was
placed in the GC oven with constant temperature (25 °C). Helium gas was
introduced to this sample vial to carry the vapor of chlorobenzene into the ion
source through an capillary guard column. This arrangement maintained a
steady-state pressure of chlorobenzene in the source. The filament current was
set to 6.5 A Ions were formed for various lengths of time after which the ions
were immediately extracted and the abundances of the major ions (mlz 112 and
77) were determined. The results of this experiment are shown in Figure 5-7(a).
The ion abundance follow a consistent growth with increasing ionization time as
discussed below.

To separately determine the trapping efficiency and the nature of the ion
loss, a series of experiments were performed in which an adjustable delay time
was introduced between ion formation and ion extraction. In Figure 5-7(b), the
measured abundance of the chlorobenzene ions are shown as a function of the
delay time after an ionization time of 142 us. In this experiment, essentially no
ion loss is observed. Repeating this same experiment after an ionization time of
342 us (Figure 5-7(c)) again shows no loss for periods up to 475 us. From this

experiment, it seems clear that the loss mechanism observed during ion

157

Sum of m/z 77 and 112

 

 

 

 

 

 

 

 

:— /
60 r (a) a
I: ”/1" m/z112
30 i ’/ .//::r~*tr7”‘
L filzjzér/ m/z 77
L at
0 :- ff
0 A 100 A 200 A 300 A 400
Ionization time (us)
5‘
g 35 __
8 Z ~+__* + m/z112
:6 20 :- ‘,AA\‘\:___——-‘—A———‘/"\A—————L——A
x ‘_ mlz 77
‘1‘? : (b)
o r . a . - . - . - a . .
o 100 200 300 400 500
m/z112
35 i" +’;:::::::+_+\‘\+—+———+N_+___d+.~.——-+K+
:- A ‘—‘\A—_E-/&\‘MJ——A——A
T mh77
20 :'
: (C)
E
0 .

o ‘106 ‘260 A 360‘ 460 A560
Delay time between ionization and
extraction (us)

Figure 5-7. The abundance of the major ions of chlorobenzene as a
function of (a) continuous ionization time and (b) extraction delays after an
ionization time of 142 us and (c) 342 us. The RF applied is 600 volts
(peak to peak) and 1.2 MHz.

158

formation is related to processes occurring during the ionization, not to
processes occurring during ion storage.

A further study in the dynamics of the increases in ion population in the
trap as a function of ionization time was undertaken. In this case PFTBA was
chosen for the analyte so that a wide range of mlz values would be represented.
Oven temperature was varied to change the concentrations of PFTBA introduced
into the ion source. The abundance of the major ions of PFTBA as a function of
ionization time for three 60 oven temperatures is shown in Figure 5-8. The
curves represented by different symbols are actually data points for ions with
different mlz values. The population growth curves follow a first order loss

against a constant rate of generation according to the equation:

(1%, = k, p — k,N (equation 2)
where N is the ion abundance, k, and k, are the formation and loss rate constants
and p is the sample pressure. The experimental data points in the first 380 us

ionization time(except the data in Figure 5-8(c)) in Figure 8 are fit to the

integrated form of equation 3 shown below.
’9 -t, .
N = 7(- p(1 - e ) (equatlon 3)
I

The goodness of this fit confirms that a constant rate of ion formation is
countered by a loss mechanism whose rate is proportional to the total number of
ions in the trap. The time constant ilk, for the resulting best-fit exponential

growth curves of the different m/z values is from 200 to 300 us. As shown in

25

30

Peak area (ns V)

01
O

 

159

m/z 69 Oven temperature: 25 °C
m/z 100 (a)
mlz 1 31
m/z 129

mlz 262

  
  
  
   
 

>I<><

 

I'lfifjlrj

 

 

0 1 00 - 200 300 400

x m [2 69 Oven temperature: 34°C
v mlz 100

I mlz 131 (b)
A mlz 129
mlz 262

   
  
  
   

0 1 00 200 300 400

mlz 69 Oven temperature: 44°C
mlz 100 ('x

m/z 131 (C)
m/z 129

mlz 262

   
  
   

>I<X

«L

+++++

4* l L n

0 1 00 200 300 400
Ionization time (us)

Figure 5-8. Ion build-up curves of major ions of PFTBA at oven temperatures of
(a) 25°C, (b) 34° C, and (c) 44’ C.

160

Figure 5-8, most of the ions are continuously accumulated in the ion source. Ion
formation rate is increased by increasing oven temperature from 25 0C to 34 °C,
but the relative intensity of these ion peaks is almost the same. When the oven
temperature is increased to 44 °C as shown in Figure 5-8 (c), the abundance of
the m/z 264 and 219 ions diminishes after 200 us. This indicates that some kind
of ion-molecule reaction becomes significant in the ion source when the sample
pressure is increased. Although a clean picture of the ion loss mechanism can
not be drawn, it is important to note that if extraction is accomplished within the
first 200 us of ionization, the relative ion abundance remains a reproducible
parameter, characteristic of the sample molecule and amenable for quantitation.
The advantage of this fact for GC chromatographic detection is further discussed

in a later section.

5.4 Interface between gas chromatograph and the SRSITOF mass

spectrometer

5. 4. 1 Dynamic working curve and Detection limit

Overall instrument performance for sensitivity and dynamic range was tested by
obtaining a working curve as shown in Figure 5-9. The analyte for this study was
chlorobenzene. A volume of 1 ul of chlorobenzene in hexane solvent was
injected into the gas chromatograph operating in the split injection mode. Analyte
concentrations varied from 20 ng/ul to tong/pl. The column was a HP-5 capillary

column of 10 m length , 0.1 mm inner diameter and 0.17 um film thickness. The

 

161

total flow rate of helium was set at 50 ml/min. The volumetric flow rate of 0.091
mein is calculated by following equation3
Volumetric Flow Rate (ml/min)= 0.785x(D2L/t,)
Where : D(mm) is column diameter

L(m) is the column length

t,(min) is the retention time of an unretained components
measured.

A linear range was confirmed from 36 pg to 18 ng as shown in Figure 5-9.
The detection limit was first evaluated by injecting 1ul of chlorobenzene at a
concentration of 20 ng/ul. The split ratio of 1:550 was used. The reconstructed
ion chromatogram from mlz=112 of the 36 pg sample injection is shown in Figure
5-10. A peak-finding technique was used to differentiate the signal peak and
background noise in the individual mass spectrum. In Figure 5-11 the major
peak of the mass spectrum of chlorobenzene taken at spectrum number 19 is
shown. Each mass spectrum was the sum of 256 transients. The signal to noise
ratio of greater than 3 was obtained for this 36 pg sample at a spectral
generation rate of 4 spectra per second.

These data were collected with an ionization time of 100 us and an
extraction rate of 1000 Hz. They verify the earlier assumption that at 100 us
ionization time, the trapped ion population is a valid measure of the amount of
sample being introduced into the source. Better results could be obtained with

an extraction rate of 6 kHz which is the reciprocal of the maximum ion flight time.

162

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In our current system, the maximum extraction frequency is limited by the nature
of the RF generator and the transient recorder used and not by the ion storage,
extraction, and focusing optics. Achievement of the maximum extraction rate of 6
kHz would provide the same signal to noise ratio obtained for the 36 pg of
chlorobenzene in Figure 11, but at 24 spectra per second. Conversely, the better
sensitivity obtained with the 6 kHz extraction at a lower number of spectra per
second will improve ion statistics at the limit of detection increasing the linear
range of measurement.

The RF voltage applied to the ring electrode elements in the above
experiments was 600 VW. The source vacuum chamber pressure was
approximately 2 x1043 torr. Each MCP plate had a voltage of 800 V across it and
the detector gain was limited by the background (especially the helium) ions.
These low mass ions continuously leave the source and a significant portion of
them reaches the detector. The resulting background current has a high level of
shot noise and limits the usable detector gain.

An ion deflector which consists of two parallel stainless steel plates
described in Chapter 4 was added along the ion flight path. A pulsed voltage (up
to 850 V higher than the field free region voltage), synchronized with the
ionization period, can be applied to one deflection plate while the other
deflection plate remains at the field free region potential. This has the dual effect
of lowering the background current and allowing a much higher gain in the

electron multiplier detector. The anode current of the detector was decreased to

166

less than 1x10‘A, even when each MCP plate of the detector had 980 V across
it. The improvement afforded is shown by the test below.

Thirty-six picograms of chlorobenzene were introduced into the mass
spectrometer by injecting 1 pl of a solution of analyte concentrations of 20 ng/ul
through a gas chromatograph with a split ratio of 1:550. The Reconstructed Ion
Chromatograph (RIC) of m/z 112 is shown in Figure 5-12 and the mass spectrum
of the chlorobenzene at spectrum no. 34 (background subtracted) is shown in
Figure 5-13. The peaks shown are due to the chlorobenzene and background
chemical noise. The instmmental noise relative to the mlz 112 peak of
chlorobenzene is about 2%. This suggests a detection limit with a SIM of 50 at

about 36 pg.

5.4.2 Advantage of less Interference from Ion/molecule reactions

As several researchers have addressed" 5' °- 7- °- 9

, the problem of the
occurrence of ion molecule reactions during GC/MS analysis with a conventional
quadrupole mass spectrometer complicates the unambiguous identification of
the compounds as well as affecting the accuracy of quantitative analysis. The
occurrence of such reactions (commonly termed as self chemical ionization),
results in excessive [M+1]“/M+ ratios and other adduct peaks for many classes of
compounds that are analyzed typically by GC/MS. McLuckey and Glish et al.
showed that the extent of the ion/molecule reaction in the ion trap can be

minimized by either reducing the amount of sample introduced or reducing the

trap time between ionization and ion analysis’. Yost et al.3 demonstrated that

 

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169

the ion/molecule reaction could be eliminated by using external electron
ionization for benzophenone at least up to 500 ng.

For the SRS-TOF mass spectrometer operated at an extraction frequency
of 5 kHz, ions would be stored in the ion source for only 200 us. Benzophenone,
a compound very prone to self-Cl in normal ion trap spectra, was used to
evaluate the self-chemical ionization interference in the SRS ion source. Analyte
concentrations varied from 0.55 mg/ml to 55 mg/ml. With a split ratio of 1:550, 1
ng to 100 ng benzophenone was introduced into the mass spectrometer for
each tul injection. Because the Precision Instrument transient recorder board
can only be used for a signal intensity up to 1 V, the detector gain was set low
by applying 720 V across each MCP plate. The linear relationship between the
peak areas of the mlz 77, 105, 182, 183 at the maximum chromatographic
elution concentration position and the amount of sample injected is shown in
Figure 5-14(a). The peak area ratios of [M+1]*/M* versus the amount of sample
introduced into the mass spectrometer are shown in Figure 5-14 (b). The peak
area ratio closely follows the isotopic ratio of 14.5% of the molecular ions of
benzophenone up to at least a 100 ng sample introduction. As the sample
introduced increases from 5 ng to 100 ng, no adduct ions are observed.

Yost et al.9 showed that the peak ratio of the [M+1]*/[M]" increased
linearly with the amount of benzophenone injected and it reaches a ratio more
than 0.6:1 when 50 ng of analyte was injected into a normal ion trap . The self-

chemical ionization did not happen in his external electron ionization ITMS. Both

170

 

 

 

 

 

 

 

 

 

 

 

10000 L Peak area vs. Sample amount I
L mlz105
32‘ L (a)
33 g ;
m ..
o. E -
3 r
E mlz 183
o L . .
O 100
100.
E 0.. . [M+1]"'/[M]+ vs. samlple amount
1: :2: -
3 I? (b) -..- Experimental Value
3 g r -——- ‘- Theoritical Value
8 i-
Q l—
. :07— — ~ -1
O 1 . 1 - l . 1 . 1 - l
0 20 40 6O 80 . 100

Sample amount (ng)

Figure 5-14. The intensity of major ions of benzophenone vs. amount
of sample introduced (a) and the peak area ratio of [M+1] lfM] 6f
bezophenone vs. amount of sample introduced (b).

171

1000 ~

400.‘ J
7i

 

 

(a)
MSDB Spectrum
of Benzophenone

 

100

 

 

 

200 300
25000 7
r (D)
20000 E 100 ng Benzophenone
:_ Lfrom SRSITOF-MS
0 : .‘—‘— - - ..‘.IL._ 3‘ I _ -___-.-__:.._--_,.:. ._
g 500 — (c)
g f 1 ng Benzophenone
+5 T from SRSfTOF-MS
200_

 

 

 

 

 

:J-j

 

(d)

500 ng Benzophenone
from external El ITMS

 

 

100

200 300

Figure 5-15. Spectra of Benzophenone obtained from different instruments.
(a) MSDB data base. (b) and (c) SRS/T OF mass spectrometer. (d) ITMS with

external electron impact ionization.

172

the external electron impact ionization ITMS and our SRS-TOF/MS can generate
mass spectra without self-chemical ionization interference for higher analyte
concentrations. The mass spectrum of benzophenone obtained from Mass
Spectral Data Base (MSDB)‘°, our instrument and an External Ionization ITMS6
are shown in Figure 5-15. The mass spectrum obtained from the SRS-TOF mass
spectrometer has a relative abundance similar to the MSDB spectrum for
existing ion peaks. The experimental results documented above demonstrate
that the SRSITOF-MS provides a characteristic mass spectrum even at high

sample concentrations and without adjustment of ionization time.

References:

 

1 Hart, K. 1.; McLuckey, S. A.; Glish, G. L.: Proc. 39th ASMS Conf. Mass
Spectrometry and Allied Topics, Nashville, 1991 p. 1495.

2 Mather, R. E., Waldren, R. M., Todd, J. F. J., and March, R. E.: Some
Operational Characteristics of a Quadrupole Ion Storage Mass Spectrometer Having
Cylindrical Geometry. Int. J. Mass Spectrom. Ion Phys. 33, 201-230 (1980).

3 Operating Manual for HP 5 890 Series 11 Gas Chromatograph. Hewlett Packard,
chapter 4, p11, October (1991)

4Pannell, L. K, Pu, Q. L., Fales, H. M., Mason, R. T., and Stephenson, Jr.; Anal.
Chem., 61, 2500-2503 (1989)

5 Ratnayake, W. M. N.; Timmins, A.; Ohshima, T,; Ackman, R. G.; Lipids. 21,
518-524 (1986)

6Olson, E. 8.; Diehl, J. W.; Anal Chem., 59, 443-448 (1987)

7Mcluckey, S. A., Glish, G. L., Asano, K. G.; Van Berke], G. J.; Anal. Chem, 60,
2312-2314 (1988)

173

 

1'Booth, M. M. , Stephenson, J. L. J., and Yost, R. A.; Proc. 41st ASMS Conf.
Mass Spectrometry and Allied Topics. San Francisco p.716a (1993)

9Yates, N. A., Booth, M. M., Stephenson Jr., J. L. and Yost R. A.: Practical
Aspects of Ion Trap Mass Spectrometry, Vol. 3, 121-186, CRC Press (1995)

1° MSDB, NIST Standard Reference Database Series la, the NIST/EPA/MSDC
Mass Spectral Database Version 3.02, June (1990)

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Chapter 6 Significance and potential advantages for SRS/T OF

mass spectrometer as a detector for chromatography

The segmented ring trap with its cylindrical geometry exhibits the ability to trap
ions and hold them for several hundred microseconds or more. The mass range
of entrapment closely follows the expected stability diagram for the cylindrical
ion trap which, for the parameters used, closely follows the classical quadrupole
equations as well. The fields are surely not perfectly quadrupolar, but perfectly
quadrupolar fields are not required for broad mass range ion storage, only for
selective mlz value rejection.

The uniform extraction fields possible with this geometry enable good
mass resolution to be achieved without the need for ion cooling prior to mass
analysis. The high voltage extraction is designed to minimize the effect of the
turn around time on the mass resolution. For electron impact ionization, It was
discovered that the best RF phase angle for application of the DC extraction
pulse is 270°. At this RF phase angle, ions will be at their lowest field-induced
kinetic energy state. Also at this RF phase angle, the direction of the DC
extraction voltage is same as the direction of the RF voltage change. A general
method which guides the construction of a reflectron that is able to focus
isomass ions with a broad energy distribution, due to RF trapping field and high
extraction voltage, was developed. Unit mass resolution for mlz 502 has been

obtained with this non-optimized prototype instrument.

175

Without component optimization, the present unit readily generates
information for up to 1000 spectra per second. As shown in Figures 5-7 and 5-8,
population growth is still in the nearly linear phase at a 100 us ionization and
storage time. Analytically reliable linear growth to this point is confirmed by the
data in Figure 59 where a series of varying analyte concentrations show a
linear response of ion population to concentration with this ionization timing.

With a 100 as ionization time and a 1 kHz extraction rate, the sample
utilization duty cycle is very nearly 10%. With improved electronics and
adjustments to the source design, one can realistically envision a continuous
sample duty cycle approaching 100% for chromatographic applications. A high
ion compaction value is achieved; all the ions of each mlz value generated
during 100 us arrive at the detector within approximately 80 ns. This gives rise to
an instantaneous peak detector current that is 1200 times greater than that
produced by the average ion generation rate. A signal to noise ratio more than
10:1 for 7 pg of chlorobenzene will be readily achievable with a clean vaCuum
system (reduction of chemical noise) as shown in Figure 5-13. With optimization
of ion optics and improvements in electronic design, the SRS-TOF mass
spectrometer will provide gas chromatographic detection with a speed and
sensitivity better than existing ion trap and quadrupole filter mass spectrometers
while still producing full mass range spectra.

Experimental results have also revealed that the SRS-TOF mass

spectrometer can give characteristic mass spectra for gas chromatographic

176

eluents. The obtained mass spectra exhibit no self-chemical ionization
interferences, which are a bane to normal ion trap operation, and peak relative
abundances are similar to library spectra obtained by electron impact ionization
and a scanning sector mass spectrometer.

The significance of the performance of the SRS/l' OF mass spectrometer
is that it has the potential to be a nearly ideal detector for chromatographic
separation. Consider, for example, the following categories.

a. A compact SRS/T OF mass analysis detector for fast GC/MS analysis of
trace amounts of small molecules for environmental, industrial and biomedical
applications.

The mass range of ion storage and resolution currently achieved is more
than sufficient for small molecules. With optical, mechanical and electronic
improvements, this performance could be maintained while the actual size of the
instrument could be much smaller. The ion storage capability gives good
detection limits and the absence of ion molecular reaction distortion will give a
linear response for varieties of organic compounds. The physical simplicity of
time-of—fiight mass analysis and the segmented ring ion storage source will
provide economical advantages in the commercialization of this instrument.

b. A high profile SRSfl’ OF mass spectrometer for fast gas
chromatographic detection of complex mixture analysis with the possibly a

GC/MS/MS capability.

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The speed, sensitivity and characteristic mass analysis of the SRSITOF-
MS will provide rich information for the chromatographically eluted components.
Even for unresolved peaks, the frequent and complete mass spectral information
will enable the direct application of effective mathematical routines for the
differentiation of coeluting compounds. If more segmented ring electrode
elements are used, the improved storage field could possibly allow ion selective
storage during the ionization period by adding a modulated RF signal to the ion
source end caps. This selective ion storage will provide a possible basis for the
MS/MS capability of this instrument. In an alternative mode, an interface
between this segmented ring ion trap storage source and a tandem time-of-flight
mass spectrometer will provide GC/MS/MS capability with good detection limits
on the chromatographic time scale.

c. A high profile SRS/T OF mass spectrometer for chromatographic
separations interfaced with external ionization techniques such electrospray
ionization and continuous flow matrix laser desorption.

It is quite possible that the open structure of the segmented ring ion trap
storage source will be accessible for ion introduction of externally generated
ions. The interface of condensed phase chromatography (such as liquid
chromatography and capillary electrophoresis) to the ionization techniques (such
as electrospray ionization, matrix laser desorption ionization) has increased the
demand for fast mass spectrometric detection. With improved mass range and

exploration of ion injection and continuous ion trap accumulation, a segmented

178

ring ion trap storage device should give fast, mass spectrometric detection for

these chromatographic separation techniques.

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