Associative ion-molecule reactions and ion trapping with a triple quadrupole mass spectrometer

231 Pages·1993·5.5 MB·English

by  Annacchino, Anthony Peter

'
ASSOCIATIVE ION-MOLECULE REACTIONS AND ION TRAPPING
WITH A TRIPLE QUADRUPOLE MASS SPECTROMETER
By
ANTHONY PETER ANNACCHINO, JR.
A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL
OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY
UNIVERSITY OF FLORIDA
1993
To my family with love.
ACKNOWLEDGEMENTS
I would like to extend my sincere gratitude to my research advisor, Dr.
Richard A. Yost. Had it not been for his support, guidance and patience (and a
couple of well-timed lunches at Joe's Deli), I am certain that this work would not
have been realized. I would also like to thank the members of my graduate
committee, Drs. James D. Winefordner, David H. Powell, John R. Eyler, and Charles
L. Beatty.
I would like to acknowledge the U.S. Environmental Protection Agency-
Environmental Research Laboratory/Duluth (U.S. EPA-ERL/D) for providing
financial support for much of this work. Additionally, I would like to thank Dr.
Douglas W. Kuehl of the U.S. EPA-ERL/D for helpful discussions.
I would like to thank all the members of the Yost group, past and present,
with whom I have had the pleasure to work during my time here in Gainesville. In
particular, I would like to acknowledge two of my office mates and close friends, Uli
Bernier and Rafael Vargas. In their company, I was able to enjoy this period of my
life and experience such wonders as the "foul towel" and the Bayou Plaza. Fond
memories, indeed. I would also like to thank all the friends that I have gained in
this community through music. More than once, these friends, and the music that
111
I shared with them, reinvigorated me when I needed it the most. Also, I was always
reminded that there is more to life than graduate school.
I would like to thank my family, Mom, Dad, and Ken, who supported me
throughout my studies and always had confidence in me, even during the rough
times.
Finally, I would like to express my sincere thanks and love to my fiancee,
Jennifer Buckingham. Her companionship and understanding allowed me to devote
more time to school than was fair to her. But, then again, she said I would pay later.
IV
TABLE OF CONTENTS
ACKNOWLEDGEMENTS
iii
ABSTRACT viii
CHAPTERS
INTRODUCTION
1
1
Methods for the Determination of Mutagenic Compounds 2
Ion-Molecule Reactions in the Collision Cell of a
Triple Quadrupole Mass Spectrometer 3
Trapping Ions with Linear RF-only Multipole Devices 5
Organization of Dissertation 10
REACTIONS OF DNA/RNA BASE AND
2
NUCLEOSIDE IONS WITH ALLYL HALIDES 13
Introduction 13
Ionization of DNA/RNA Bases and Nucleosides 13
Technique of Performing Ion-Molecule Reactions in Q2 16
Experimental 18
Chemicals 18
Instrumentation 18
Procedures 21
Reactions of DNA/RNA Base and Nucleoside Ions
with Allyl Halides 22
Selection of Molecular Ions or Protonated
Molecules for Reactions 22
DNA/RNA
Relative Reactivities of Base
and Nucleoside Ions 26
Correlation of Reactivities to Mutagenicities 37
Identification and Correlation of Side Reaction Products 39
Reactions of Guanine Ions with Allyl Halides 49
DNA/RNA
Comparison of Reactivities of Base and Nucleoside
Ions Towards Allyl Halides to Those of Pyridine Ions 52
Conclusions 55
PRACTICAL ASPECTS OF REACTIONS OF DNA/RNA BASE
AND NUCLEOSIDE IONS WITH ALLYL HALIDES 56
Introduction 56
Pressure Effects of Allyl Halides on Formation of Product Ions
DNA/RNA
upon Reaction with Base Ions 57
Experimental 57
Reactions of Uracil Ions with Allyl Halides 58
DNA/RNA
Calibration Studies of Reactions of Base Ions
with Allyl Halides 64
Experimental 64
Evaluation of Sensitivity Measurements 64
Effect of Uracil N+ Ion Intensity on Product Ion Formation 66
. .
Calibration Studies of Allyl Halides 68
Conclusions 75
DEVELOPMENT AND CHARACTERIZATION OF A SYSTEM
FOR TRAPPING IONS IN THE COLLISION CELL OF
A TRIPLE QUADRUPOLE MASS SPECTROMETER 77
Introduction 77
MAT
The Finnigan TSQ70 Triple Quadrupole
Mass Spectrometer 78
Trapping Ions in the Collision Cell of the TSQ70 83
Experimental 87
Experimental Conditions 87
Determination of Ion Trapping Efficiencies 89
TSQ70 Timing Studies 92
Methods for Trapping Ions in Q2 98
Precursory Techniques 98
External Control of the Exit Lens (L31) for
Enhanced Ion Detection 105
Helium Buffer Gas Effects Ill
Pressure Studies 114
Ion Trapping Efficiencies 116
Optimization of Ion Optics for Q2 Trapping 122
Entrance Lens, L23 122
Collision (Q2) Offset Potential 128
Instrument Tuning for Q2 Ion Trapping 130
Conclusions 134
VI
INVESTIGATIONS OF ION TRAPPING: FUNDAMENTAL
5
STUDIES AND APPLICATIONS FOR ENHANCEMENT
OF ASSOCIATIVE ION-MOLECULE REACTIONS 136
Introduction 136
Experimental 137
Optimization of Mass Scanning Parameters 140
Ion Accumulation in the Collision Cell 142
Fill Time Studies 154
Trapping Time Studies 158
Full Scan Data while Trapping Ions in Q2 167
DNA/RNA
Reactions of Base Ions with Allyl Chloride
under Ion Trapping Conditions 172
Conclusions 180
6 CONCLUSIONS AND FUTURE WORK 183
Conclusions 183
Suggestions for Future Work 187
Reactions of Other Nucleophile Ions 187
Comparison of Quadrupole and Octopole Collision Cells .... 188
Radial Detection of Stored Ions via RF Ramping 188
Replacement of Q3 with a Quadrupole Ion Trap
(Q-Q-ITMS) 191
Resonance Excitation in Q2 192
APPENDICES
A TUNING GUIDELINES FOR LOW-ENERGY
ION-MOLECULE REACTIONS AND ION TRAPPING
IN THE COLLISION CELL OF THE TSQ70 195
B INSTRUMENT CONTROL LANGUAGE (ICL) PROCEDURES
USED TO FACILITATE TUNING FOR ION TRAPPING
IN THE COLLISION CELL OF THE TSQ70 200
C INSTRUMENT CONTROL LANGUAGE (ICL) PROCEDURES
USED TO PERFORM ION TRAPPING IN THE COLLISION
CELL OF THE TSQ70 206
LITERATURE CITED 212
BIOGRAPHICAL SKETCH 219
vn
Abstract of Dissertation Presented to the Graduate School
of the University of Florida in Partial Fulfillment of the
Requirements for the Degree of Doctor of Philosophy
ASSOCIATIVE ION-MOLECULE REACTIONS AND ION TRAPPING
WITH A TRIPLE QUADRUPOLE MASS SPECTROMETER
By
Anthony Peter Annacchino, Jr.
December 1993
Chairperson: Dr. Richard A. Yost
Major Department: Chemistry
DNA/RNA
Gas-phase reactions of ionized bases and nucleosides with
electrophilic allyl halides in the collision cell of a triple quadrupole mass
spectrometer have been demonstrated. Reactions of this type are important because
of their correspondencewith the reactions of mutagenic electrophileswith biological
DNA/RNA
macromolecules in vivo. Relative reactivities ofthe base and nucleoside
ions toward the allyl halides were determined based on the production of allyl-
nucleophile adduct ions, P+ Side reaction products due to charge exchange
.
processes were also observed for many of the reagent combinations. Significant
intensities of side reaction products were typically observed only when allyl iodide
was used as the electrophile; in many cases the abundance of side reaction products
distorted the relative reactivity as measured by P+ production. Calibration curves for
vm
reactions of each DNA/RNA base ion with allyl halides were generally not linear;
DNA/RNA
limits of detection for the most reactive base ion, uracil, were on the
order of 10-100 femtomoles of allyl halide.
A
system for trapping ions in the collision cell of a triple quadrupole mass
spectrometer has been developed and characterized. Mass-selected ions are injected
into the collision cell and trapped within Q2 for a variable period of time.
Subsequently, the ions are gated out of Q2 and mass-analyzed by Q3. Ion optical
parameters significant for effective ion trapping have been detailed and optimized.
Moreover, the importance of helium buffer gas to Q2 ion trapping has been
demonstrated via calculations of ion trapping efficiencies. It has been determined
that buffer gas can enhance ion confinement and detection by over 2000%.
Utilizing the Q2 ion trapping system, applications have been demonstrated
that illustrate the power and utility of the technique. It has been shown that large
numbers of ions can be stored in the collision cell for several hours or more.
Furthermore, it was demonstrated that Q2 ion trapping can be used to study ion-
molecule reactions. In particular, the method was utilized to enhance formation of
DNA/RNA
product ions resulting from reactions of base ions with allyl chloride.
IX
CHAPTER
1
INTRODUCTION
In this dissertation studies are presented that demonstrate the utility of
associative ion-molecule reactions and ion trapping with a triple quadrupole mass
spectrometer (TQMS). Gas-phase reactions of DNA/RNA base and nucleoside ions
with electrophilic allyl halides have been studied as an extension of previous work
[1] done in our laboratory involving ion-molecule reactions of various electrophiles
with small model bases such as pyridine and piperidine. The studies presented here
have shown that, while the reactions are often complex, characteristic product ions
can signal the presence of potential carcinogens. Furthermore, the method can be
used to roughlyestimate the relative reactivities ofthese potential carcinogens. Also,
TQMS
a technique for ion trapping in the collision cell of the has been developed
and characterized. The method allows execution of experiments that are normally
impractical, or impossible, to perform on standard tandem quadrupole instruments.
In particular, the technique is useful for the study of kinetically slow ion-molecule
reactions.
Thisintroductorychapterbeginswith a review ofvariousanalytical techniques
that have been utilized for the determination ofmutagenic compounds. It continues
with a short discussion of ion-molecule reactions in the collision cell of the TQMS.
A
summary of previous research involving ion trapping with linear RF-only