Mass Spectrometry A Textbook, 2nd Edition Jurgen H. Gross

Mass Spectrometry
Second Edition



Jürgen H. Gross

Mass Spectrometry
A Textbook
Second Edition

Foreword by Peter Roepstorff

123


Jürgen H. Gross
Institute of Organic Chemistry
Heidelberg University
Im Neuenheimer Feld 270
69120 Heidelberg
Germany
email:

ISBN 978-3-642-10709-2
e-ISBN 978-3-642-10711-5
DOI 10.1007/978-3-642-10711-5
Springer Heidelberg Dordrecht London New York
c Springer-Verlag Berlin Heidelberg 2004, 2011
This work is subject to copyright. All rights are reserved, whether the whole or part of the material is

concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,
reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication
or parts thereof is permitted only under the provisions of the German Copyright Law of September 9,
1965, in its current version, and permission for use must always be obtained from Springer. Violations
are liable to prosecution under the German Copyright Law.
The use of general descriptive names, registered names, trademarks, etc. in this publication does not
imply, even in the absence of a specific statement, that such names are exempt from the relevant protective
laws and regulations and therefore free for general use.
Cover design: WMXDesign GmbH, Heidelberg
Printed on acid-free paper
Springer is part of Springer Science+Business Media (www.springer.com)


Foreword

Shortly after having graduated in 1966 and just employed as a research assistant in
a protein chemistry laboratory, my very first contact with mass spectrometry happened when I stumbled on a paper by Michael Barber, the later discoverer of fast
atom bombardment (FAB). Together with a French group he had determined the
covalent structure of an almost 1.4 kDa complex peptidolipid called fortuitine by
using mass spectrometry. Fascinated by this to me unknown technique, I felt that
MS would be a future key analytical method in protein studies. At that time, the
only ionization method available was electron ionization, which required a sample
to be in the gaseous state in the ion source. Therefore most mass spectrometric
analyses were dealing with small organic molecules – and peptides and proteins
were not volatile. Fortuitine was a very fortuitous sample, because it was naturally
derivatized with the consequence that it could be volatilized into the ion source.
Nevertheless, I went into mass spectrometry. My first mass spectrometer was installed in our laboratory in 1968. Mass spectrometers at that time were complex
fully manually operated instruments most of them magnetic/electrostatic sector instruments, and the operator needed to know the instrument well in order to avoid
catastrophes by opening wrong valves at the wrong moment. Spectra were recorded on UV paper with a galvanometer recorder or on photographic plates and
mass assignment was performed manually. During the 1970s a number of new

ionization methods and mass analyzers became available. These included ionization by chemical ionization and by field ionization/desorption as well as mass
analyses by quadrupoles and ion traps. Computers became available for data acquisition and mass assignment. Life became easier but the requirement for volatile
samples was still there.
The 1980s revolutionized the possibilities for mass spectrometric analysis. In
the early half of the decade introduction of FAB and commercialization of the 10
years earlier developed plasma desorption mass spectrometry allowed for analyses
of nonvolatile samples such as peptides, proteins, and nucleic acids. The first
commercial fully automated mass spectrometer, the BioIon plasma desorption
mass spectrometer, became available and the time-of-flight analyzer, which had
unlimited mass range, was revived. Late in the decade the two new and now
dominating ionization methods electrospray ionization (ESI) and matrix-assisted
laser desorption ionization (MALDI) were introduced. These two ionization methods opened a new era for mass spectrometry. Now all the large nonvolatile biological molecules could be analyzed. Till then GC-MS had been extensively used
for analysis of complex mixtures in environmental and clinical sciences, but due
to its nature it was limited to small volatile molecules. ESI made coupling of LC
with MS possible allowing for entirely new applications of mass spectrometry.
Proteomics now became a big move forward with mass spectrometry as the key
analytical tool. Thousands of scientists took up mass spectrometric analysis and


VI

Foreword

the instrument manufacturers realized that a new market had emerged and that the
new generation of users were different from the previous technically skilled specialists. The new generation of instruments therefore became computer controlled,
equipped with safety features to avoid any erroneous operation and with fully
computerized data acquisition. The requirement from the biological sciences for
high speed, sensitivity, and mass accuracy resulted in dramatic improvements of
the performance of the instruments. Hybrid instruments combining the wellknown mass analyzers were constructed, the FT-ICR mass spectrometer, which till
then had only been available in highly specialized mass spectrometry laboratories,

moved into the biological laboratory. Lately, the orbitrap analyzer, also based on
Fourier transformation, has become standard in advanced biological research laboratories. Biological mass spectrometry and especially analysis of proteins and proteomics now dominate mass spectrometry conferences and mass spectrometry has
a strong position in biological conferences, where these subjects ten years earlier
were only marginally present.
What are the consequences of this development? For me, having tried to get
mass spectrometry into protein science for more than 40 years it is of course encouraging. Mass spectrometry is without any doubt now the most versatile analytical technique available. It is used in a wide variety of areas from inorganic, nuclear chemistry, and geochemistry over organic chemistry, environmental
analyses, clinical chemistry, to molecular and cell biology. Online separation of
complex mixtures is possible using either GC-MS or LC-MS. Almost all commercial instruments are highly automated. However, this development also rises serious concerns. Many of the new users consider the mass spectrometer as a black
box where they put in the sample in one end and get a result from the computer in
the other end. They do not or only marginally understand the principles in their instrument and rarely look at the raw data. They are satisfied with computer prints
with lists of identified compounds. Sample preparation often follows standard protocols and the understanding of the need for optimized sample preparation for
each analytical task is often ignored. As a result, a considerable amount of the data
obtained are questionable either due to poor sample preparation, poor instrument
performance, or suboptimal use of the instruments. It is my wish that the new generation of mass spectrometry users will spend time to understand their instruments
and the requirements for optimal preparation of the samples and it is my hope that
this book will be read by many of them so that they can use their techniques to the
best of the equipment’s potential.
Odense, 2010
Peter Roepstorff
Department of Biochemistry and Molecular Biology
University of Southern Denmark


Preface to the Second Edition

To all readers of the first edition of Mass Spectrometry – A Textbook I would like
to express my deepest gratitude. Without their interest in wanting to learn more
about mass spectrometry by use of this book, all the efforts in writing it would
have been a mere waste of time, and moreover, without their demand for updates,
there would be no next edition. I would also like to thank the instructors all over

the world who adopted and recommended this book for their own mass spectrometry courses.
Preparing the second edition of Mass Spectrometry – A Textbook was not an
easy task. The years have witnessed a flood of innovations and detailed knowledge of interrelationships that were previously hardly understood. The time between the editions may have appeared a bit long for many eager scholars. But the
author has used the time effectively to improve and update the entire contents,
hopefully to the benefit of all who have been patiently bearing with me in anticipation.
So, what’s new? The book now comprises fifteen instead of twelve chapters,
each of them headed by essential “Learning Objectives”. Chapter 9 inserts methods of ion activation such as CID, ECD, ETD, and IRMPD closely related to the
instrumental approaches to tandem mass spectrometry. A second additional chapter deals with sampling and ion generation from surfaces under ambient conditions
as afforded by DART and DESI, to name the most relevant methods. Finally, a
new chapter on inorganic mass spectrometry has been added, for one, to include
element speciation that bridges the gap between biomedical and trace elemental
analysis and, also, to open a perspective extending beyond the key topics of this
book. The chapter on instrumentation has been significantly expanded to cover orbitrap, linear ion traps, TOF/TOF, FT-ICR, and the ever-changing hybrid instruments including IMS-MS systems. More detailed attention is drawn to applications regarding biopolymers, especially in those chapters dealing with MALDI
and ESI.
Overall, the book has been expanded by more than 200 pages. No chapter has
remained untouched. Numerous passages have been rewritten to improve the clarity of explanations while keeping them short and concise. Care has been taken not
only to explain how, but also to why things are done a certain way. Several
schemes have been added to clarify interrelationships between different techniques. Tables compiling data for general reference where transferred to the expanded appendix. The book’s website has been updated providing new exercises
and supplementary material ().


VIII

Preface to the Second Edition

Many kind people have supported me in the process of compiling this second
edition. I appreciate the detailed knowledge and great thoroughness of Kenzo Hiraoka, Yasuhide Naito, Takemichi Nakamura, and Hiroaki Sato allocated to the
translation of the first edition into Japanese. The valuable and welcome comments
from readers from all over the world, and in particular, from book reviewers and
colleagues have revealed some shortcomings in the first edition, which now have

been eliminated to the improvement of the resulting new edition.
As in the first edition, several well-respected colleagues have contributed to
this book by carefully checking contents in their fields of expertise. For the second
edition, I want to express special thanks to Jürgen Grotemeyer, Universität Kiel,
for checking Chap. 2 (Principles of Ionization and Ion Dissociation), Alexander
Makarov, Thermo Fisher Scientific, Bremen (Chap. 4, Instrumentation), Christoph
A. Schalley, Freie Universität Berlin (Chap. 9, Tandem Mass Spectrometry), Belá
Paizs, German Cancer Research Center, Heidelberg (Chap. 11, Matrix-Assisted
Laser Desorption/Ionization), Zoltán Takáts, Universität Gießen (Chap. 13, Ambient Mass Spectrometry), and Detlef Günther, ETH Zürich (Chap. 15, Inorganic
Mass Spectrometry). Without their care and help the many new parts would not
have reached the present level of accuracy. Despite intense reviewing and proofreading some errors inevitably may have remained. I apologize for these in advance and would highly appreciate any feedback from the readership in trying to
identify and correcting them.
I am indebted to Peter Roepstorff, Odense University, for writing the Foreword
with such a personal connotation. Permission to prepare this 2nd edition, alongside
my official professional duties, by A. Stephen K. Hashmi, Director of OCI, and
Heinfried Schöler, Dean of the Faculty of Chemistry and Earth Sciences is sincerely acknowledged. Many thanks to Doris Lang, Iris Mitsch, and Norbert Nieth,
for smoothly running the routine analyses in our MS facility. And again, several
mass spectrometry companies are acknowledged for supplying new instrument
schemes and other figures for inclusion in the 2nd edition. Theodor C. H. Cole accomplished a great job in polishing up my English. Finally, I am immeasurably
grateful to my family for their patience and solidarity in times when I had to come
home late or needed to vanish on Saturdays during the writing of this book.
Have a good time studying, learning, and enjoying the world of mass
spectrometry!
Heidelberg, 2010
Jürgen H. Gross
Institute of Organic Chemistry
Heidelberg University
Im Neuenheimer Feld 270
69120 Heidelberg
Germany

email:


Preface

When non-mass spectrometrists are talking about mass spectrometry it rather often
sounds as if they were telling a story out of Poe's Tales of Mystery and Imagination. Indeed, mass spectrometry appears to be regarded as a mysterious method,
just good enough to supply some molecular weight information. Unfortunately,
this rumor about the dark side of analytical methods reaches students much earlier
than their first contact with mass spectrometry. Possibly, some of this may have
been bred by mass spectrometrists themselves who tended to celebrate each mass
spectrum they obtained from the gigantic machines of the early days. Of course,
there were also those who enthusiastically started in the 1950s to develop mass
spectrometry out of the domain of physics to become a new analytical tool for
chemistry.
Nonetheless, some oddities remain and the method which is to be introduced
herein is not always straightforward and easy. If you had asked me, the author,
just after having finished my introductory course whether mass spectrometry
would become my preferred area of work, I surely would have strongly denied.
On the other hand, J. J. Veith's mass spectrometry laboratory at Darmstadt University was bright and clean, had no noxious odors, and thus presented a nice contrast
to a preparative organic chemistry laboratory. Numerous stainless steel flanges
and electronics cabinets were tempting to be explored and – whoops – infected me
with CMSD (chronic mass spectrometry disease). Staying with Veith's group
slowly transformed me into a mass spectrometrist. Inspiring books such as
Fundamental Aspects of Organic Mass Spectrometry or Metastable Ions, out of
stock even in those days, did help me very much during my metamorphosis. Having completed my doctoral thesis on fragmentation pathways of isolated immonium ions in the gas phase, I assumed my current position. Since 1994, I have
been head of the mass spectrometry laboratory at the Chemistry Department of
Heidelberg University where I teach introductory courses and seminars on mass
spectrometry.
When students ask what books to read on mass spectrometry, there are various

excellent monographs, but the ideal textbook still seemed to be missing – at least
in my opinion. Finally, encouraged by many people including P. Enders, SpringerVerlag Heidelberg, two years of writing began.
The present volume would not have its actual status without the critical reviews
of the chapters by leading experts in the field. Their thorough corrections, remarks, and comments were essential. Therefore, P. Enders, Springer-Verlag Heidelberg (Introduction), J. Grotemeyer, University of Kiel (Gas Phase Ion Chemistry), S. Giesa, Bayer Industry Services, Leverkusen (Isotopes), J. Franzen, Bruker


X

Preface

Daltonik, Bremen (Instrumentation), J. O. Metzger, University of Oldenburg
(Electron Ionization and Fragmentation of Organic Ions and Interpretation of EI
Mass Spectra), J. R. Wesener, Bayer Industry Services, Leverkusen (Chemical
Ionization), J. J. Veith, Technical University of Darmstadt (Field Desorption),
R. M. Caprioli, Vanderbilt University, Nashville (Fast Atom Bombardment),
M. Karas, University of Frankfurt (Matrix-Assisted Laser Desorption/Ionization),
M. Wilm, European Molecular Biology Laboratory, Heidelberg (Electrospray
Ionization) and M. W. Linscheid, Humboldt University, Berlin (Hyphenated
Methods) deserve my deep gratitude.
Many manufacturers of mass spectrometers and mass spectrometry supply are
gratefully acknowledged for sending large collections of schemes and photographs
for use in this book. The author wishes to express his thanks to those scientists,
many of them from the University of Heidelberg, who generously allowed to use
material from their actual research as examples and to those publishers, who
granted the numerous copyrights for use of figures from their publications. The
generous permission of the National Institute of Standards and Technology
(G. Mallard, J. Sauerwein) to use a large set of electron ionization mass spectra
from the NIST/EPA/NIH Mass Spectral Library is also gratefully acknowledged.
My thanks are extended to the staff of my facility (N. Nieth, A. Seith, B. Flock)
for their efforts and to the staff of the local libraries for their friendly support. I am

indebted to the former director of our institute (R. Gleiter) and to the former dean
of our faculty (R. N. Lichtenthaler) for permission to write a book besides my official duties.
Despite all efforts, some errors or misleading passages will still have remained.
Mistakes are an attribute that make us human, but unfortunately, they do not contribute to the scientific or educational value of a textbook. Therefore, please do not
hesitate to report errors to me or to drop a line of comment in order to allow for
corrections in a future edition.
Hopefully, Mass Spectrometry – A Textbook will introduce you to the many
facets of mass spectrometry and will satisfy your expectations.
Heidelberg, 2003
Jürgen H. Gross
Institute of Organic Chemistry
Heidelberg University
Im Neuenheimer Feld 270
69120 Heidelberg
Germany
email:


Table of Contents

Table of Contents................................................................................................ XI
1 Introduction ........................................................................................................1
Learning Objectives ......................................................................................1
1.1 Aims and Scope ...........................................................................................3
1.1.1 Filling the Black Box ...........................................................................5
1.2 What Is Mass Spectrometry? .......................................................................5
1.2.1 Mass Spectrometry ...............................................................................6
1.2.2 Mass Spectrometer ...............................................................................7
1.2.3 Mass Scale............................................................................................8
1.2.4 Mass Spectrum .....................................................................................9

1.3 Ion Chromatograms ...................................................................................11
1.4 Performance of Mass Spectrometers..........................................................13
1.4.1 Sensitivity...........................................................................................13
1.4.2 Detection Limit ..................................................................................14
1.4.3 Signal-to-Noise Ratio .........................................................................14
1.5 Terminology – General Aspects ................................................................15
1.5.1 Basic Terminology in Describing Mass Spectra ................................16
1.6 Units, Physical Quantities, and Physical Constants ...................................17
References........................................................................................................17
2 Principles of Ionization and Ion Dissociation.................................................21
Learning Objectives ....................................................................................21
2.1 Gas Phase Ionization by Energetic Electrons.............................................21
2.1.1 Formation of Ions ...............................................................................22
2.1.2 Processes Accompanying Electron Ionization....................................23
2.1.3 Ions Generated by Penning Ionization................................................24
2.1.4 Ionization Energy ...............................................................................25
2.1.5 Ionization Energy and Charge-Localization.......................................25
2.2 Vertical Transitions....................................................................................27
2.3 Ionization Efficiency and Ionization Cross Section...................................29


XII

Table of Contents

2.4 Internal Energy and the Further Fate of Ions ............................................. 30
2.4.1 Degrees of Freedom ........................................................................... 31
2.4.2 Appearance Energy ............................................................................ 32
2.4.3 Bond Dissociation Energies and Heats of Formation......................... 33
2.4.4 Randomization of Energy................................................................... 35

2.5 Quasi-Equilibrium Theory......................................................................... 37
2.5.1 QET’s Basic Premises........................................................................ 37
2.5.2 Basic QET .......................................................................................... 38
2.5.3 Rate Constants and Their Meaning .................................................... 39
2.5.4 k(E) Functions – Typical Examples ..................................................... 40
2.5.5 Reacting Ions Described by k(E) Functions ......................................... 40
2.5.6 Direct Cleavages and Rearrangement Fragmentations....................... 40
2.6 Time Scale of Events ................................................................................. 42
2.6.1 Stable, Metastable, and Unstable Ions................................................ 43
2.6.2 Time Scale of Ion Storage Devices .................................................... 44
2.7 Internal Energy – Practical Implications.................................................... 45
2.8 Reverse Reactions and Kinetic Energy Release ........................................ 46
2.8.1 Activation Energy of the Reverse Reaction ....................................... 46
2.8.2 Kinetic Energy Release ...................................................................... 48
2.8.3 Energy Partitioning ............................................................................ 49
2.9 Isotope Effects ........................................................................................... 49
2.9.1 Primary Kinetic Isotope Effects ......................................................... 50
2.9.2 Measurement of Isotope Effects......................................................... 51
2.9.3 Secondary Kinetic Isotope Effects ..................................................... 53
2.10 Determination of Ionization Energies...................................................... 54
2.10.1 Conventional Determination of Ionization Energies ........................ 54
2.10.2 Improved IE Accuracy from Data Post-Processing.......................... 54
2.10.3 IE Accuracy – Experimental Improvements .................................... 55
2.10.4 Photoionization Processes ................................................................ 55
2.11 Determining the Appearance Energies .................................................... 58
2.11.1 Kinetic Shift ..................................................................................... 58
2.11.2 Breakdown Graphs........................................................................... 59
2.12 Gas Phase Basicity and Proton Affinity................................................... 61
References ....................................................................................................... 62
3 Isotopic Composition and Accurate Mass ...................................................... 67

Learning Objectives .................................................................................... 67
3.1 Isotopic Classification of the Elements...................................................... 67
3.1.1 Monoisotopic Elements . ..................................................................... 68
3.1.2 Di-isotopic Elements .......................................................................... 68
3.1.3 Polyisotopic Elements ........................................................................ 69
3.1.4 Representation of Isotopic Abundances ............................................. 69
3.1.5 Calculation of Atomic, Molecular, and Ionic Mass............................ 71
3.1.6 Natural Variations in Relative Atomic Mass...................................... 73
3.2 Calculation of Isotopic Distributions ......................................................... 74
3.2.1 Carbon: An X+1 Element................................................................... 74


Table of Contents

XIII

3.2.2 Terms Related to Isotopic Composition .............................................77
3.2.3 Binomial Approach ............................................................................77
3.2.4 Halogens.............................................................................................78
3.2.5 Combinations of Carbon and Halogens..............................................80
3.2.6 Polynomial Approach.........................................................................81
3.2.7 Oxygen, Silicon, and Sulfur ...............................................................81
3.2.8 Polyisotopic Elements ........................................................................84
3.2.9 Practical Aspects of Isotopic Patterns ................................................84
3.2.10 Bookkeeping with Isotopic Patterns in Mass Spectra.......................85
3.2.11 Information from Complex Isotopic Patterns ...................................86
3.3 Isotopic Enrichment and Isotopic Labeling ...............................................87
3.3.1 Isotopic Enrichment ...........................................................................87
3.3.2 Isotopic Labeling................................................................................88
3.4 Resolution and Resolving Power ...............................................................88

3.4.1 Definitions..........................................................................................88
3.4.2 Resolution and its Experimental Determination.................................90
3.4.3 Resolving Power and its Effect on Relative Peak Intensity................91
3.5 Accurate Mass ...........................................................................................92
3.5.1 Exact Mass and Molecular Formulas .................................................92
3.5.2 Mass Defect........................................................................................93
3.5.3 Mass Accuracy ...................................................................................95
3.5.4 Accuracy and Precision ......................................................................96
3.5.5 Mass Accuracy and the Determination of Molecular Formulas .........97
3.5.6 Extreme Mass Accuracy – Special Considerations ............................98
3.6 Applied High-Resolution Mass Spectrometry ...........................................99
3.6.1 External Mass Calibration ..................................................................99
3.6.2 Internal Mass Calibration .................................................................101
3.6.3 Compiling Mass Reference Lists......................................................103
3.6.4 Specification of Mass Accuracy .......................................................104
3.6.5 Deltamass .........................................................................................104
3.6.6 Kendrick Mass Scale ........................................................................105
3.6.7 Van Krevelen Diagrams ...................................................................106
3.7 Resolution Interacting with Isotopic Patterns ..........................................107
3.7.1 Multiple Isotopic Compositions at Very High Resolution ...............107
3.7.2 Isotopologs and Accurate Mass........................................................110
3.7.3 Large Molecules – Isotopic Patterns at Sufficient Resolution..........110
3.7.4 Large Molecules – Isotopic Patterns at Low Resolution.......... ........ 112
3.8 Charge State and Interaction with Isotopic Patterns ................................112
References......................................................................................................114
4 Instrumentation ..............................................................................................117
Learning Objectives ..................................................................................117
4.1 How to Create a Beam of Ions.................................................................119
4.2 Time-of-Flight Instruments......................................................................120
4.2.1 Time-of-Flight – Basic Principles ....................................................120

4.2.2 TOF Instruments – Velocity of Ions and Time-of-Flight .................121
4.2.3 Linear Time-of-Flight Analyzer .......................................................123


XIV

Table of Contents

4.2.4 Reflector Time-of-Flight Analyzer .................................................. 126
4.2.5 Higher Vacuum Improves Resolving Power.................................... 128
4.2.6 Delay Before Extraction to Improve Resolving Power .................... 128
4.2.7 Analog-to-Digital Conversion.......................................................... 131
4.2.8 Orthogonal Acceleration TOF Analyzers......................................... 132
4.2.9 Operation of the oaTOF Analyzer.................................................... 133
4.2.10 Duty Cycle ..................................................................................... 134
4.2.11 Time-to-Digital Conversion ........................................................... 135
4.3 Magnetic Sector Instruments ................................................................... 135
4.3.1 Evolution of Magnetic Sector Instruments....................................... 135
4.3.2 Principle of the Magnetic Sector ...................................................... 136
4.3.3 Focusing Action of the Magnetic Field ............................................ 138
4.3.4 Double-Focusing Sector Instruments ............................................... 139
4.3.5 Geometries of Double-Focusing Sector Instruments........................ 141
4.3.6 Adjusting the Resolving Power of a Sector Instrument.................... 143
4.3.7 Innovations in Sector Instruments.................................................... 144
4.4 Linear Quadrupole Instruments ............................................................... 146
4.4.1 Introduction ...................................................................................... 146
4.4.2 The Linear Quadrupole .................................................................... 147
4.4.3 Resolving Power of Linear Quadrupoles ......................................... 151
4.4.4 RF-Only Quadrupoles, Hexapoles, and Octopoles........................... 152
4.5 Linear Quadrupole Ion Traps................................................................... 155

4.5.1 Linear RF-Only Multipole Ion Traps ............................................... 155
4.5.2 Mass-Analyzing Linear Quadrupole Ion Trap with Axial Ejection . 158
4.5.3 Mass-Analyzing Linear Ion Trap with Radial Ejection.................... 160
4.6 Three-Dimensional Quadrupole Ion Trap................................................ 164
4.6.1 Introduction ...................................................................................... 164
4.6.2 The Quadrupole Ion Trap ................................................................. 164
4.6.3 Visualization of Ion Motion in the Ion Trap .................................... 167
4.6.4 Mass-Selective Stability Mode......................................................... 168
4.6.5 Mass-Selective Instability Mode ...................................................... 168
4.6.6 Resonant Ejection............................................................................. 169
4.6.7 Axial Modulation and Automatic Gain Control ............................... 170
4.6.8 Nonlinear Resonances ...................................................................... 171
4.6.9 Digital Waveform Quadrupole Ion Trap .......................................... 172
4.6.10 External Ion Sources for the Quadrupole Ion Trap ........................ 173
4.7 Fourier Transform Ion Cyclotron Resonance .......................................... 174
4.7.1 Ion Cyclotron Resonance ................................................................. 174
4.7.2 Ion Cyclotron Motion....................................................................... 174
4.7.3 Cyclotron Motion – Excitation and Detection.................................. 175
4.7.4 Cyclotron Frequency Bandwidth and Energy-Time Uncertainty ..... 177
4.7.5 Fourier Transform – Basic Properties .............................................. 179
4.7.6 Nyquist Criterion.............................................................................. 181
4.7.7 Excitation Modes in FT-ICR-MS..................................................... 182
4.7.8 Axial Trapping and Design of ICR Cells ......................................... 183
4.7.9 Magnetron Motion and Reduced Cyclotron Frequency ................... 184


Table of Contents

XV

4.7.10 Detection and Accuracy in FT-ICR-MS.........................................186
4.7.11 FT-ICR Instruments .......................................................................187
4.8 Orbitrap Analyzer ....................................................................................189
4.8.1 Orbitrap – Principle of Operation.....................................................189
4.8.2 Ion Detection and Resolving Power of the Orbitrap ........................191
4.8.3 Ion Injection into the Orbitrap..........................................................192
4.8.4 Hybridization with a Linear Quadrupole Ion Trap ...........................193
4.9 Hybrid Instruments ..................................................................................194
4.9.1 Evolution of Hybrid Mass Spectrometers.........................................196
4.9.2 Ion Mobility-Mass Spectrometry Systems .......................................198
4.10 Detectors ................................................................................................202
4.10.1 Discrete Dynode Electron Multipliers............................................203
4.10.2 Channel Electron Multipliers .........................................................204
4.10.3 Microchannel Plates .......................................................................205
4.10.4 Post-Acceleration and Conversion Dynode....................................206
4.10.5 Focal Plane Detectors.....................................................................207
4.11 Vacuum Technology..............................................................................208
4.11.1 Basic Mass Spectrometer Vacuum System ....................................209
4.11.2 High Vacuum Pumps......................................................................209
4.12 Purchasing an Instrument.......................................................................210
References......................................................................................................210
5 Practical Aspects of Electron Ionization.......................................................223
Learning Objectives ..................................................................................223
5.1 Electron Ionization Ion Sources...............................................................223
5.1.1 Layout of an Electron Ionization Ion Source....................................223
5.1.2 Generation of Primary Electrons ......................................................225
5.1.3 Overall Efficiency and Sensitivity of an El Ion Source....................226
5.1.4 Optimization of Ion Beam Geometry ...............................................227
5.2 Sample Introduction.................................................................................228
5.2.1 Reservoir or Reference Inlet System ................................................228

5.2.2 Direct Insertion Probe ......................................................................231
5.2.3 Sample Vials for Use with Direct Insertion Probes..........................232
5.2.4 Fractionation When Using Direct Insertion Probes..........................233
5.2.5 Direct Exposure Probe......................................................................235
5.3 Pyrolysis Mass Spectrometry...................................................................237
5.4 Gas Chromatograph .................................................................................237
5.5 Liquid Chromatograph.............................................................................238
5.6 Low-Energy Electron Ionization Mass Spectra .......................................239
5.7 Analytes for EI.........................................................................................241
5.8 Mass Analyzers for EI .............................................................................241
5.9 Mass Spectral Databases for EI ...............................................................242
5.9.1 NIST/EPA/NIH Mass Spectral Database .........................................243
5.9.2 Wiley Registry of Mass Spectral Data .............................................244
5.9.3 Mass Spectral Databases – General Aspects ....................................244
References......................................................................................................245


XVI

Table of Contents

6 Fragmentation of Organic Ions and Interpretation of EI Mass Spectra ... 249
Learning Objectives .................................................................................. 249
6.1 Cleavage of a Sigma-Bond ...................................................................... 250
6.1.1 Writing Conventions for Molecular Ions ......................................... 250
6.1.2 σ-Bond Cleavage in Small Nonfunctionalized Molecules ............... 251
6.1.3 Even-Electron Rule .......................................................................... 252
6.1.4 σ-Bond Cleavage in Small Functionalized Molecules ..................... 254
6.2 Alpha-Cleavage ....................................................................................... 255
6.2.1 α-Cleavage of Acetone Molecular Ion............................................. 255

6.2.2 Stevenson's Rule............................................................................... 257
6.2.3 α-Cleavage of Nonsymmetrical Aliphatic Ketones.......................... 259
6.2.4 Acylium Ions and Carbenium Ions................................................... 260
6.2.5 α-Cleavage When Heteroatoms Belong to the Aliphatic Chain....... 262
6.2.6 α-Cleavage of Aliphatic Amines...................................................... 262
6.2.7 Nitrogen Rule ................................................................................... 265
6.2.8 α-Cleavage of Aliphatic Ethers and Alcohols.................................. 266
6.2.9 Charge Retention at the Heteroatom ................................................ 268
6.2.10 α-Cleavage of Thioethers............................................................... 269
6.2.11 α-Cleavage of Halogenated Hydrocarbons .................................... 269
6.2.12 Double α-Cleavage ........................................................................ 271
6.2.13 Double α-Cleavage for the Identification of Regioisomers ........... 272
6.3 Distonic Ions............................................................................................ 273
6.3.1 Definition of Distonic Ions............................................................... 273
6.3.2 Formation and Properties of Distonic Ions....................................... 274
6.3.3 Distonic Ions as Intermediates ......................................................... 275
6.4 Benzylic Bond Cleavage.......................................................................... 275
6.4.1 Cleavage of the Benzylic Bond in Phenylalkanes ............................ 275
6.4.2 The Further Fate of [C6H5]+ and [C7H7]+.......................................... 277
6.4.3 Isomerization of [C7H8]+• and [C8H8]+• Ions..................................... 279
6.4.4 Rings Plus Double Bonds................................................................. 280
6.5 Allylic Bond Cleavage............................................................................. 281
6.5.1 Cleavage of the Allylic Bond in Aliphatic Alkenes ......................... 281
6.5.2 Methods for the Localization of the Double Bond ........................... 283
6.6. Cleavage of Non-Activated Bonds ......................................................... 284
6.6.1 Saturated Hydrocarbons ................................................................... 284
6.6.2 Carbenium Ions ................................................................................ 286
6.6.3 Very Large Hydrocarbons ................................................................ 287
6.6.4 Recognition of the Molecular Ion Peak............................................ 288
6.7 McLafferty Rearrangement...................................................................... 290

6.7.1 McL of Aldehydes and Ketones....................................................... 290
6.7.2 Fragmentation of Carboxylic Acids and Their Derivatives.............. 293
6.7.3 McL of Aromatic Hydrocarbons ...................................................... 296
6.7.4 McL with Double Hydrogen Transfer.............................................. 297
6.8 Retro-Diels-Alder Reaction ..................................................................... 300
6.8.1 Properties of the Retro-Diels-Alder Reaction .................................. 300


Table of Contents XVII

6.8.2 Influence of Positional Isomerism on the RDA Reaction.................302
6.8.3 RDA Reaction in Natural Products ..................................................303
6.8.4 Widespread Occurrence of the RDA Reaction.................................303
6.9 Elimination of Carbon Monoxide ............................................................304
6.9.1 CO Loss from Phenols .....................................................................304
6.9.2 CO and C2H2 Loss from Quinones ...................................................307
6.9.3 Fragmentation of Arylalkylethers.....................................................308
6.9.4 CO Loss from Transition Metal Carbonyl Complexes.....................310
6.9.5 CO Loss from Carbonyl Compounds ...............................................311
6.9.6 Differentiation Between Loss of CO, N2, and C2H4 .........................311
6.10 Thermal Degradation vs. Ion Fragmentation .........................................312
6.10.1 Decarbonylation and Decarboxylation ...........................................312
6.10.2 Retro-Diels-Alder Reaction............................................................312
6.10.3 Loss of H2O from Alkanols............................................................312
6.10.4 EI Mass Spectra of Organic Salts ...................................................314
6.11 Alkene Loss from Onium Ions...............................................................315
6.11.1 McL of Onium Ions........................................................................316
6.11.2 Onium Reaction..............................................................................319
6.12 Ion-Neutral Complexes..........................................................................322
6.12.1 Evidence for the Existence of Ion-Neutral Complexes ..................322

6.12.2 Attractive Forces in Ion-Neutral Complexes..................................323
6.12.3 Criteria for Ion-Neutral Complexes................................................324
6.12.4 Ion-Neutral Complexes of Radical Ions .........................................325
6.13 Ortho Elimination (Ortho Effect) ..........................................................326
6.13.1 Ortho Elimination from Molecular Ions.........................................327
6.13.2 Ortho Elimination from Even-Electron Ions ..................................328
6.13.3 Ortho Elimination in the Fragmentation of Nitroarenes.................331
6.14 Heterocyclic Compounds.......................................................................332
6.14.1 Saturated Heterocyclic Compounds ...............................................333
6.14.2 Aromatic Heterocyclic Compounds ...............................................336
6.15 Guide to the Interpretation of Mass Spectra ..........................................340
6.15.1 Summary of Rules ..........................................................................340
6.15.2 Systematic Approach to Mass Spectra ...........................................341
References......................................................................................................342
7 Chemical Ionization........................................................................................351
Learning Objectives ..................................................................................351
7.1 Basics of Chemical Ionization .................................................................351
7.1.1 Formation of Ions in Positive-Ion Chemical Ionization ...................351
7.1.2 Chemical Ionization Ion Sources......................................................352
7.1.3 Sensitivity of Chemical Ionization ...................................................353
7.1.4 Chemical Ionization Techniques and Terms ....................................353
7.2 Protonation in Chemical Ionization .........................................................354
7.2.1 Source of Protons .............................................................................354
7.2.2 Methane Reagent Gas Plasma ..........................................................355
7.2.3 CH5+ and Related Ions......................................................................356


XVIII

Table of Contents

7.2.4 Energetics of Protonation ................................................................. 356
7.2.5 Impurities of Higher PA than the Reagent Gas ................................ 357
7.2.6 Methane Reagent Gas PICI Spectra ................................................. 358
7.2.7 Other Reagent Gases in PICI............................................................ 359
7.3 Proton Transfer Reaction Mass Spectrometry ......................................... 361
7.3.1 Reactant Ion Formation in PTR-MS ................................................ 362
7.3.2 Analyte Ion Formation in PTR-MS.................................................. 362
7.4 Charge Exchange Chemical Ionization.................................................... 364
7.4.1 Energetics of CE .............................................................................. 365
7.4.2 Reagent Gases for CE-CI ................................................................. 365
7.4.3 Compound Class-Selective CE-CI ................................................... 366
7.4.4 Regio- and Stereoselectivity in CE-CI ............................................. 368
7.5 Negative-Ion Chemical Ionization........................................................... 368
7.6 Electron Capture ...................................................................................... 370
7.6.1 Ion Formation by Electron Capture.................................................. 370
7.6.2 Energetics of EC .............................................................................. 370
7.6.3 Creating Thermal Electrons ............................................................. 372
7.6.4 Appearance of EC Spectra ............................................................... 373
7.6.5 Applications of EC ........................................................................... 373
7.7 Desorption Chemical Ionization .............................................................. 374
7.8 Analytes for CI ........................................................................................ 375
References ..................................................................................................... 376
8 Field Ionization and Field Desorption .......................................................... 381
Learning Objectives .................................................................................. 381
8.1 Field Ionization Process........................................................................... 382
8.2 FI and FD Ion Sources............................................................................. 383
8.3 Field Emitters .......................................................................................... 385
8.3.1 Blank Metal Wires as Emitters......................................................... 385
8.3.2 Activated Emitters............................................................................ 385

8.3.3 Emitter Temperature ........................................................................ 386
8.3.4 Handling of Activated Emitters........................................................ 387
8.4 Field Ionization Mass Spectrometry ........................................................ 388
8.4.1 Origin of [M+H]+ Ions in FI-MS...................................................... 389
8.4.2 Multiply-Charged Ions in FI-MS ..................................................... 389
8.4.3 Field-Induced Dissociation .............................................................. 390
8.4.4 Accurate Mass FI Spectra ................................................................ 390
8.4.5 Coupling Gas Chromatography to FI-MS ........................................ 391
8.5 FD Spectra ............................................................................................... 392
8.5.1 Ion Formation by Field Ionization in FD-MS .................................. 393
8.5.2 Desorption of Preformed Ions in FD-MS......................................... 394
8.5.3 Cluster Ion Formation in FD-MS ..................................................... 396
8.5.4 FD-MS of Ionic Analytes ................................................................. 397
8.5.5 Best Anode Temperature and Thermal Decomposition ................... 399
8.5.6 FD-MS of Polymers ......................................................................... 400
8.5.7 Types of Ions in FD-MS................................................................... 401


Table of Contents

XIX

8.6 Liquid Injection Field Desorption Ionization...........................................402
8.7 General Properties of FI-MS and FD-MS................................................405
8.7.1 Sensitivity of FI-MS and FD-MS .....................................................405
8.7.2 Analytes and Practical Considerations for FI, FD, and LIFDI .........407
8.7.3 Mass Analyzers for FI and FD .........................................................407
References......................................................................................................408
9 Tandem Mass Spectrometry..........................................................................415
Learning Objectives ..................................................................................415

9.1 Concepts of Tandem Mass Spectrometry ................................................415
9.1.1 Tandem-in-Space and Tandem-in-Time...........................................416
9.1.2 Pictograms for MS/MS Experiments................................................418
9.2 Metastable Ion Dissociation.....................................................................420
9.3 Collision-Induced Dissociation................................................................420
9.3.1 Effecting Collisions in a Mass Spectrometer....................................420
9.3.2 Energy Transfer During Collisions...................................................421
9.3.4 Single and Multiple Collisions in CID .............................................424
9.3.5 Time Scale of Ion Activating Processes ...........................................426
9.4 Surface-Induced Dissociation ..................................................................426
9.5 Tandem MS on TOF Instruments ............................................................427
9.5.1 Utilizing a ReTOF for Tandem MS..................................................427
9.5.2 Curved-Field Reflectron...................................................................429
9.5.3 Tandem MS on True Tandem TOF Instruments ..............................429
9.6 Tandem MS with Magnetic Sector Instruments.......................................431
9.6.1 Dissociations in the FFR Preceding the Magnetic Sector.................431
9.6.2 Mass-Analyzed Ion Kinetic Energy Spectra.....................................432
9.6.3 Determination of Kinetic Energy Release ........................................432
9.6.4 B/E = Const. Linked Scan ................................................................434
9.6.5 Additional Linked Scan Functions ...................................................434
9.6.6 Multi-Sector Instruments..................................................................436
9.7 Tandem MS with Linear Quadrupole Analyzers .....................................437
9.7.1 Triple Quadrupole Mass Spectrometers ...........................................437
9.7.2 Scan Modes for Tandem MS with Triple Quadrupole Instruments..438
9.7.3 Penta Quadrupole Instruments .........................................................438
9.8 Tandem MS with the Quadrupole Ion Trap .............................................439
9.9 Tandem MS with Linear Quadrupole Ion Traps ......................................443
9.9.1 Tandem MS on QqLIT Instruments .................................................444
9.9.2 Tandem MS on LITs with Radial Ejection.......................................444
9.10 Tandem MS with Orbitrap Instruments .................................................445

9.10.1 Higher-Energy C-Trap Dissociation...............................................446
9.10.2 Extended LIT-Orbitrap Hybrid Instruments...................................446
9.11 Tandem MS with FT-ICR Instruments – Part I .....................................448
9.11.1 Sustained Off-Resonance Irradiation-CID in ICR Cells.................448
9.12 Infrared Multiphoton Dissociation.........................................................451
9.12.1 IRMPD in QITs and LITs...............................................................452
9.13 Electron Capture Dissociation ...............................................................452


XX

Table of Contents

9.13.1 Principles of Electron Capture Dissociation................................... 452
9.13.2 Peptide Ion Cleavages Upon ECD ................................................. 454
9.14 Tandem MS with FT-ICR Instruments – Part II .................................... 455
9.14.1 IRMPD for Tandem FT-ICR-MS................................................... 455
9.14.2 Infrared Photodissociation Spectroscopy ....................................... 456
9.14.3 Blackbody Infrared Radiative Dissociation.................................... 457
9.14.4 ECD for Tandem FT-ICR-MS ....................................................... 458
9.15 Electron Transfer Dissociation .............................................................. 459
9.16 Electron Detachment Dissociation......................................................... 461
9.17 Summary of Ion Activation Techniques ................................................ 462
9.18 Special Applications of Tandem MS ..................................................... 463
9.18.1 Ion–Molecule Reactions in Catalytic Studies................................. 464
9.18.2 Gas Phase Hydrogen–Deuterium Exchange................................... 464
9.18.3 Determination of Gas Phase Basicities and Proton Affinities ........ 466
9.18.4 Neutralization-Reionization Mass Spectrometry............................ 467
References ..................................................................................................... 468
10 Fast Atom Bombardment ............................................................................ 479

Learning Objectives .................................................................................. 479
10.1 Ion Sources for FAB and LSIMS .......................................................... 480
10.1.1 FAB Ion Sources ............................................................................ 480
10.1.2 LSIMS Ion Sources ........................................................................ 482
10.1.3 FAB Probes .................................................................................... 482
10.2 Ion Formation in FAB and LSIMS ........................................................ 483
10.2.1 Ion Formation from Inorganic Samples ......................................... 483
10.2.2 Ion Formation from Organic Samples............................................ 484
10.3 Liquid Matrices for FAB and LSIMS.................................................... 486
10.3.1 The Role of the Liquid Matrix ....................................................... 486
10.3.2 FAB Matrix Spectra – General Characteristics .............................. 487
10.3.3 Unwanted Reactions in FAB-MS................................................... 487
10.4 Applications of FAB-MS....................................................................... 488
10.4.1 FAB-MS of Analytes of Low to Medium Polarity......................... 488
10.4.2 FAB-MS of Ionic Analytes ............................................................ 490
10.4.3 High-Mass Analytes in FAB-MS ................................................... 491
10.4.4 Accurate Mass Measurements in FAB Mode................................. 492
10.4.5 Continuous-Flow FAB ................................................................... 494
10.4.6 Low-Temperature FAB .................................................................. 495
10.4.7 FAB-MS and Peptide Sequencing.................................................. 496
10.5 FAB and LSIMS – General Characteristics........................................... 496
10.5.1 Sensitivity of FAB-MS................................................................... 496
10.5.2 Types of Ions in FAB-MS .............................................................. 497
10.5.3 Analytes for FAB-MS .................................................................... 497
10.5.4 Mass Analyzers for FAB-MS......................................................... 497
10.6 Massive Cluster Impact ......................................................................... 498
10.7 252Californium Plasma Desorption......................................................... 498
References ..................................................................................................... 499

Table of Contents

XXI

11 Matrix-Assisted Laser Desorption/Ionization ............................................507
Learning Objectives ..................................................................................507
11.1 Ion Sources for LDI and MALDI ..........................................................508
11.2 Ion Formation ........................................................................................509
11.2.1 Ion Yield and Laser Fluence...........................................................510
11.2.2 Effect of Laser Irradiation on the Surface ......................................511
11.2.3 Temporal Evolution of a Laser Desorption Plume .........................512
11.2.4 Processes of Ion Formation in MALDI ..........................................513
11.2.5 “Lucky Survivor” Model of Ion Formation....................................514
11.3 MALDI Matrices ...................................................................................516
11.3.1 Role of the Solid Matrix .................................................................516
11.3.2 Matrices in UV-MALDI.................................................................516
11.3.3 Characteristics of MALDI Matrix Spectra .....................................519
11.4 Sample Preparation ................................................................................519
11.4.1 MALDI Target ...............................................................................519
11.4.2 Standard Sample Preparation .........................................................520
11.4.3 Cationization ..................................................................................522
11.4.4 Cation Removal..............................................................................524
11.4.5 Solvent-Free Sample Preparation ...................................................526
11.4.6 Additional Methods of Sample Supply ..........................................527
11.5 Applications of LDI ...............................................................................527
11.6 Applications of MALDI.........................................................................529
11.6.1 Protein Analysis by MALDI-MS ...................................................529
11.6.2 Peptide Sequencing and Proteomics...............................................531
11.6.3 Carbohydrate Analysis by MALDI-MS .........................................536
11.6.4 Oligonucleotide Analysis by MALDI-MS .....................................538

11.6.5 MALDI-MS of Synthetic Polymers ...............................................539
11.7 Special Surfaces to Mimic the Matrix....................................................541
11.7.1 Desorption/Ionization on Silicon....................................................541
11.7.2 Nano-Assisted Laser Desorption/Ionization...................................542
11.7.3 Further Variations of the MALDI Theme ......................................543
11.8 MALDI Imaging ....................................................................................544
11.9 Atmospheric Pressure MALDI ..............................................................546
11.10 General Characteristics of MALDI......................................................547
11.10.1 Sample Consumption and Detection Limit...................................547
11.10.2 Analytes for MALDI ....................................................................547
11.10.3 Types of Ions in LDI and MALDI-MS ........................................548
11.10.4 Mass Analyzers for MALDI-MS..................................................548
References......................................................................................................549
12 Electrospray Ionization................................................................................561
Learning Objectives ..................................................................................561
12.1 Development of ESI and Related Methods............................................562
12.1.1 Atmospheric Pressure Ionization....................................................563
12.1.2 Thermospray...................................................................................564
12.1.3 Electrohydrodynamic Ionization ....................................................565


XXII

Table of Contents

12.1.4 Electrospray Ionization .................................................................. 565
12.2 Ion Sources for ESI................................................................................ 566
12.2.1 Basic Design Considerations.......................................................... 566
12.2.2 Adaptation to Different Flow Rates ............................................... 568
12.2.3 Improved Electrospray Configurations .......................................... 569

12.2.4 Advanced Electrospray Interface Designs...................................... 571
12.2.5 Nozzle-Skimmer Dissociation........................................................ 573
12.3 Nanoelectrospray ................................................................................... 574
12.3.1 Practical Considerations for NanoESI............................................ 575
12.3.2 Spray Modes of NanoESI............................................................... 576
12.3.3 Nanoelectrospray from a Chip ....................................................... 577
12.4 Ion Formation in ESI ............................................................................. 578
12.4.1 Formation of the Electrospray Plume............................................. 578
12.4.2 Disintegration of Charged Droplets................................................ 581
12.4.3 Formation of Ions from Charged Droplets ..................................... 582
12.5 Multiply Charged Ions and Charge Deconvolution ............................... 585
12.5.1 Dealing with Multiply Charged Ions.............................................. 585
12.5.2 Mathematical Charge Deconvolution............................................. 587
12.5.3 Computerized Charge Deconvolution ............................................ 588
12.5.4 Hardware Charge Deconvolution ................................................... 590
12.5.5 Controlled Charge Reduction in ESI.............................................. 592
12.6 Applications of ESI-MS ........................................................................ 593
12.6.1 ESI-MS of Small Molecules........................................................... 593
12.6.2 ESI of Metal Complexes ................................................................ 594
12.6.3 ESI of Surfactants........................................................................... 596
12.6.4 Oligonucleotides, DNA, and RNA................................................. 596
12.6.5 ESI-MS of Oligosaccharides .......................................................... 599
12.6.6 High-Mass Proteins and Protein Complexes .................................. 600
12.7 Summary of ESI Characteristics............................................................ 601
12.7.1 Sample Consumption ..................................................................... 603
12.7.2 Types of Ions in ESI....................................................................... 603
12.7.3 Mass Analyzers for ESI.................................................................. 603
12.8 Atmospheric Pressure Chemical Ionization........................................... 604
12.8.1 Ion Sources for APCI ..................................................................... 604
12.8.2 Ion Formation in APCI................................................................... 605

12.8.3 APCI Spectra.................................................................................. 605
12.9 Atmospheric Pressure Photoionization .................................................. 608
12.9.1 Ion Formation in APPI ................................................................... 608
12.9.2 APPI Spectra .................................................................................. 610
References ..................................................................................................... 612
13 Ambient Mass Spectrometry ....................................................................... 621
Learning Objectives .................................................................................. 621
13.1 Desorption Electrospray Ionization ....................................................... 622
13.1.1 Experimental Setup for DESI......................................................... 622
13.1.2 Mechanisms of Ion Formation in DESI.......................................... 626


Table of Contents

XXIII

13.1.3 Analytical Features of DESI...........................................................627
13.2 Desorption Atmospheric Pressure Chemical Ionization ........................631
13.3 Desorption Atmospheric Pressure Photoionization ...............................632
13.4 Other Methods Related to DESI ............................................................634
13.4.1 Desorption Sonic Spray Ionization.................................................635
13.4.2 Extractive Electrospray Ionization .................................................635
13.4.3 Electrospray-Assisted Laser Desorption/Ionization (ELDI)...........637
13.4.4 Laser Ablation Electrospray Ionization ..........................................638
13.4.5 Atmospheric Pressure Solids Analysis Probe.................................640
13.5 Direct Analysis in Real Time.................................................................640
13.5.1 Experimental Setup for DART.......................................................640
13.5.2 Ion Formation in DART .................................................................642
13.5.3 Analytical Applications of DART..................................................642
13.6 Overview of Ambient Mass Spectrometry .............................................644

References......................................................................................................645
14 Hyphenated Methods ...................................................................................651
Learning Objectives ..................................................................................651
14.1 Concept of Chromatography-Mass Spectrometry..................................652
14.1.1 Ion Chromatograms........................................................................653
14.1.2 Repetitive Acquisition of Mass Spectra During Elution ................654
14.1.3 Selected Ion Monitoring .................................................................656
14.1.4 Selected Reaction Monitoring ........................................................658
14.2 Quantitation ...........................................................................................659
14.2.1 Quantitation by External Standardization.......................................659
14.2.2 Quantitation by Internal Standardization........................................660
14.2.3 Quantitation by Isotope Dilution ....................................................661
14.2.4 Retention Times of Isotopologs......................................................663
14.3 Gas Chromatography-Mass Spectrometry .............................................663
14.3.1 GC-MS Interfaces...........................................................................663
14.3.2 Volatility and Derivatization ..........................................................664
14.3.3 Column Bleed.................................................................................665
14.3.4 Fast GC-MS....................................................................................667
14.3.5 Multiplexing for Increased Throughput .........................................667
14.4 Liquid Chromatography-Mass Spectrometry.........................................668
14.4.1 Multiplexed LC-ESI-MS ................................................................671
14.5 Ion Mobility Spectrometry-Mass Spectrometry.....................................673
14.6 Tandem MS as a Complement to LC-MS .... .........................................675
14.7 Ultrahigh-Resolution Mass Spectrometry .............................................678
References......................................................................................................680
15 Inorganic Mass Spectrometry .....................................................................685
Learning Objectives ..................................................................................685
15.1 Thermal Ionization Mass Spectrometry .................................................689
15.2 Spark Source Mass Spectrometry ..........................................................691
15.3 Glow Discharge Mass Spectrometry......................................................694

XXIV

Table of Contents

15.4 Inductively Coupled Plasma Mass Spectrometry .................................. 697
15.4.1 Laser Ablation ICP-MS.................................................................. 700
15.5 Secondary Ion Mass Spectrometry ........................................................ 701
15.5.1 Atomic SIMS ................................................................................. 702
15.5.2 Instrumentation for Atomic SIMS.................................................. 702
15.5.3 Molecular SIMS ............................................................................. 704
15.5.4 Polyatomic Primary Ion Beams...................................................... 705
15.6 Accelerator Mass Spectrometry............................................................. 707
15.7 Conclusion ............................................................................................. 710
References ..................................................................................................... 711
Appendix ............................................................................................................ 717
A.1 Units, Physical Quantities, and Physical Constants ................................ 717
A.2 Isotopic Composition of the Elements .................................................... 718
A.3 Carbon Isotopic Patterns......................................................................... 725
A.4 Chlorine and Bromine Isotopic Patterns ................................................. 726
A.5 Silicon and Sulfur Isotopic Patterns........................................................ 727
A.6 Isotopologs and Accurate Mass .............................................................. 727
A.7 Characteristic Ions .................................................................................. 728
A.8 Common Impurities ................................................................................ 729
A.9 Amino Acids........................................................................................... 730
A.10 Method Selection Guide ....................................................................... 731
A.11 How to Recognize Cationization .......................................................... 732
A.12 Systematic Approach to Mass Spectra.................................................. 733
A.13 Rules for the Interpretation of Mass Spectra......................................... 733

A.14 Nobel Prizes for Mass Spectrometry .................................................... 734
Subject Index ..................................................................................................... 735