Jiirgen H. Gross. Mass Spectrometry

Transcription

1 Jiirgen H. Gross Mass Spectrometry

2 J urgen H. Gross Mass Spectrometry A Textbook With 357 Illustrations and Tables ~ Springer

3 DR. JURGEN H. GROSS Institute of Organic Chemistry University of Heidelberg 1m Neuenheimer Feld Heidelberg Germany Problems and Solutions available via author's website Library of Congress Control Number: st ed Corr. 2nd printing ISBN DOl / ISBN (ebook) This work is subject to copyright. All rights 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 for prosecution under the German Copyright Law. Springer is a part of Springer Science+Business Media springer. com Springer-Verlag Berlin Heidelberg 2004 Softcover reprint of the hardcover 1st edition 2004 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. Typesetting: Data conversion by author Production: LE-Tpc, Jelonek, Schmidt & V6ckler GbR, Leipzig Coverdesign: KiinkelLopka, Heidelberg Printed on acid-free paper 2/3100NL

4 Dedicated to my wife Michaela and my daughters Julia and Elena

5 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, Springer Verlag 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), 1. Franzen, Bruker

6 VIII 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 NISTIEPAINIH 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. Jtirgen H. Gross University of Heidelberg Institute of Organic Chemistry 1m Neuenheimer Feld Heidelberg Germany author@ms-textbook.com

7 Table of Contents Contents... IX 1 Introduction Aims and Scope... 1 l.2 What Is Mass Spectrometry? Mass Spectrometry Mass Spectrometer Mass Spectrum Filling the Black Box Terminology Units, Physical Quantities, and Physical Constants... 9 Reference List Gas Phase Ion Chemistry Quasi-Equilibrium Theory... l Basic Assumptions of QET Ionization Electron Ionization Ionization Energy Vertical Transitions Ionization Efficiency and Ionization Cross Section Internal Energy and the Further Fate oflons Degrees of Freedom Appearance Energy Bond Dissociation Energies and Heats offormation Randomization of Energy Rate Constants from QET Meaning of the Rate Constant Typical k(e) Functions Description of Reacting Ions Using k(e) Functions Direct Cleavages and Rearrangement Fragmentations Practical Consequences ofinternal Energy... 31

8 X Table of Contents 2.7 Time Scale of Events Stable, Metastable, and Unstable Ions Kinetic Shift Activation Energy of the Reverse Reaction and Kinetic Energy Release Activation Energy ofthe Reverse Reaction Kinetic Energy Release Isotope Effects Kinetic Isotope Effects Determination oflonization Energies and Appearance Energies Conventional Determination of Ionization Energies Experimental Improvements of IE Accuracy Photoelectron Spectroscopy and Derived Modem Methods Determination of Appearance Energies Breakdown Graphs Gas Phase Basicity and Proton Affinity Tandem Mass Spectrometry Collision-Induced Dissociation Other Methods of Ion Activation Reactive Collisions Reference List Isotopes Isotopic Classification of the Elements Monoisotopic Elements Di-isotopic Elements Polyisotopic Elements Calculation of Atomic, Molecular, and Ionic Mass Natural Variations in Relative Atomic Mass Calculation ofisotopic Distributions X+l Element Carbon Binomial Approach Halogens Combinations of Carbon and Halogens Polynomial Approach Oxygen, Silicon and Sulfur Polyisotopic Elements Practical Aspects of Isotopic Patterns Isotopic Enrichment and Isotopic Labeling High-Resolution and Accurate Mass Exact Mass Deviations from Nominal Mass Mass Accuracy Resolution Mass Calibration Interaction of Resolution and Isotopic Patterns Multiple Isotopic Compositions at Very High Resolution

9 XI Multiple Isotopic Compositions and Accurate Mass Isotopic Patterns of Large Molecules Interaction of Charge State and Isotopic Patterns Reference List Instrumentation Creating a Beam of Ions Time-of-Flight Instruments Introduction to Time-of-Flight Basic Principle of TOF Instruments Linear Time-of-Flight Analyzer Reflector Time-of-Flight Analyzer Further Improvement of Resolution Orthogonal Acceleration TOF Tandem MS on TOF Instruments Magnetic Sector Instruments Introduction to Magnetic Sector Instruments Principle of the Magnetic Sector Double-Focusing Sector Instruments Setting the Resolution of a Sector Instrument Further Improvement of Sector Instruments Tandem MS with Magnetic Sector Instruments Linear Quadrupole Instruments Introduction to the Linear Quadrupole Principle of the Linear Quadrupole Resolving Power of Linear Quadrupoles RF-Only Quadrupoles Tandem MS with Quadrupole Analyzers Linear Quadrupole Ion Traps Three-Dimensional Quadrupole Ion Trap Introduction to the Quadrupole Ion Trap Principle of the Quadrupole Ion Trap Operation of the Quadrupole Ion Trap External Ion Sources for the Quadrupole Ion Trap Tandem MS with the Quadrupole Ion Trap Fourier Transform Ion Cyclotron Resonance Introduction to Ion Cyclotron Resonance Principle of Ion Cyclotron Resonance Fourier Transform Ion Cyclotron Resonance Experimental Setup offt-icr-ms Excitation Modes in FT-ICR-MS Detection in FT-ICR-MS External Ion Sources for FT-ICR-MS Tandem MS with FT-ICR Instruments Hybrid Instruments Detectors

10 XII Table of Contents Discrete Dynode Electron Multipliers Channel Electron Multipliers Microchannel Plates Post-Acceleration and Conversion Dynode Focal Plane Detectors Vacuum Technology Basic Mass Spectrometer Vacuum System High Vacuum Pumps Buying an Instrument Reference List Electron Ionization Behavior of Neutrals Upon Electron Impact Formation of Ions Processes Accompanying Electron Ionization Efficiency of Electron Ionization Practical Consequences of Internal Energy Low-Energy Electron Ionization Mass Spectra Electron Ionization Ion Sources Layout of an Electron Ionization Ion Source Generation of Primary Electrons Overall Efficiency of an Electron Ionization Ion Source Optimization of Ion Beam Geometry Sample Introduction Direct Insertion Probe Direct Exposure Probe Reference Inlet System Gas Chromatograph Liquid Chromatograph Ion Chromatograms Total Ion Current Reconstructed Ion Chromatogram Mass Analyzers for EI Analytes for EI Mass Spectral Databases for EI Reference List Fragmentation of Organic Ions and Interpretation of EI Mass Spectra '" Cleavage of a Sigma-Bond Writing Conventions for Molecular Ions a-bond Cleavage in Small Non-Functionalized Molecules 'Even-Electron Rule' a-bond Cleavage in Small Functionalized Molecules Alpha-Cleavage a-cleavage of Acetone Molecular Ion Stevenson's Rule

11 XIII a-cleavage of Non-Symmetrical Aliphatic Ketones Acylium Ions and Carbenium Ions a-cleavage of Amines, Ethers, and Alcohols a-cleavage of Halogenated Hydrocarbons Double a-cleavage Distonic Ions Definition of Distonic Ions Formation and Properties of Distonic Ions Distonic Ions as Intermediates Benzylic Bond Cleavage Cleavage of the Benzylic Bond in Phenyl alkanes The Further Fate of [C6Hst and [C 7H 7t Isomerization of [C7Hst' and [CsHsr'Ions Rings Plus Double Bonds Allylic Bond Cleavage Cleavage of the Allylic Bond in Aliphatic Alkenes Methods for the Localization of the Double Bond Cleavage of Non-Activated Bonds Saturated Hydrocarbons Carbenium Ions Very Large Hydrocarbons Recognition of the Molecular Ion Peak McLafferty Rearrangement McLafferty Rearrangement of Aldehydes and Ketones Fragmentation of Carboxylic Acids and Their Derivatives McLafferty Rearrangement of Aromatic Hydrocarbons McLafferty Rearrangement with Double Hydrogen Transfer Retro-Diels-Alder Reaction Properties of the Retro-Diels-Alder Reaction Influence of Positional Isomerism on the RDA Reaction Is the RDA Reaction Stepwise or Concerted? RDA Reaction in Natural Products Widespread Occurrence of the RDA Reaction Elimination of Carbon Monoxide CO Loss from Phenols CO and C 2H 2 Loss from Quinones Fragmentation of Arylalkylethers CO Loss from Transition Metal Carbonyl Complexes CO Loss from Carbonyl Compounds Differentiation Between Loss of CO, N20 and C2H Thermal Degradation Versus Ion Fragmentation Decarbonylation and Decarboxylation Retro-Diels-Alder Reaction Loss of H 20 from Alkanols EI Mass Spectra of Organic Salts Alkene Loss from Onium Ions

12 XIV Table of Contents McLafferty Rearrangement of Onium Ions Onium Reaction Ion-Neutral Complexes Ortha Elimination (Ortha Effect) Ortha Elimination from Molecular Ions Ortha Elimination from Even-Electron Ions Ortha Elimination in the Fragmentation of Nitroarenes Heterocyclic Compounds Saturated Heterocyclic Compounds Aromatic Heterocyclic Compounds Guidelines for the Interpretation of Mass Spectra Summary of Rules Systematic Approach to Mass Spectra Reference List Chemical Ionization Basics of Chemical Ionization Formation oflons in Chemical Ionization Chemical Ionization Ion Sources Sensitivity of Chemical Ionization Chemical Ionization by Protonation Source of Protons Methane Reagent Gas Plasma Energetics of Protonation Methane Reagent Gas PICI Spectra Other Reagent Gases in PICI Charge Exchange Chemical Ionization Energetics of CE Reagent Gases for CE-CI Compound Class-Selective CE-CI Regio- and Stereoselectivity in CE-CI Electron Capture Ion Formation by Electron Capture Energetics ofec Creating Thermal Electrons Appearance of EC Spectra Applications of EC Sample Introduction in CI Desorption Chemical Ionization Analytes for CI Mass Analyzers for CI Reference List Field Ionization and Field Desorption Field Ionization Process PI and FD Ion Source

13 xv 8.3 Field Emitters Blank Metal Wires as Emitters Activated Emitters Emitter Temperature Handling of Activated Emitters Liquid Injection Field Desorption Ionization FI Spectra Origin of [M+Ht Ions in FI-MS Field-Induced Dissociation Multiply-Charged Ions in FI-MS FD Spectra Ion Formation in FD-MS Cluster Ion Formation in FD-MS FD-MS of Ionic Analytes Best Anode Temperature and Thennal Decomposition FD-MS of Polymers Sensitivity of FI-MS and FD-MS Types of Ions in FD-MS Analytes for FI and FD Mass Analyzers for FI and FD Reference List Fast Atom Bombardment Ion Sources for F AB and LSIMS FAB Ion Sources LSIMS Ion Sources FAB Probes Ion Formation in FAB and LSIMS Ion Formation from Inorganic Samples Ion Formation from Organic Samples FAB Matrices The Role of the Liquid Matrix Characteristics of FAB Matrix Spectra Unwanted Reactions in FAB-MS Applications offab-ms FAB-MS of Analytes of Low to Medium Polarity FAB-MS oflonic Analytes High-Mass Analytes in FAB-MS Accurate Mass Measurements in FAB Continuous-Flow FAB Low-Temperature FAB FAB-MS and Peptide Sequencing Massive Cluster Impact Califomium Plasma Desorption General Characteristics of FAB and LSIMS Sensitivity offab-ms

14 XVI Table of Contents Types of Ions in FAB-MS Analytes for FAB-MS Mass Analyzers for FAB-MS Reference List Matrix-Assisted Laser Desorption/Ionization Ion Sources for LOI and MALOI Ion Formation Ion Yield and Laser Fluence Effect of Laser Irradiation on the Surface Temporal Evolution of a Laser Oesorption Plume Ion Formation in MALDI MALOI Matrices Role of the Solid Matrix Matrices in UV-MALOI Characteristics ofmaldi Matrix Spectra Sample Preparation Standard Sample Preparation Cationization and Cation RemovaL Solvent-Free Sample Preparation Sample Introduction Additional Methods of Sample Supply Applications of LDI Applications of MALDI MALDI-MS of Synthetic Polymers Fingerprints by MALDI-MS Carbohydrates by MALDI-MS Structure Elucidation of Carbohydrates by MALDI Oligonucleotides in MALDI Oesorption/lonization on Silicon Atmospheric Pressure MALOI General Characteristics of MALOI Sample Consumption and Oetection Limit Analytes for MALOI Types of Ions in LDI and MALDI-MS Mass Analyzers for MALDI-MS Reference List Electrospray Ionization Oevelopment of ESI and Related Methods Atmospheric Pressure Ionization Thermospray Electrohydrodynarnic Ionization Electrospray Ionization Ion Sources for ESI Basic Oesign Considerations

15 XVII ESI with Modified Sprayers Nano-Electrospray ESI with Modified Spray Geometries Skimmer CID Ion Formation Formation of an Electrospray Disintegration of Charged Droplets Formation of Ions from Charged Droplets Charge Deconvolution Problem of Multiple Charging Mathematical Charge Deconvolution Hardware Charge Deconvolution Controlled Charge Reduction in ESI Applications of ESI ESI of Small Molecules ESI of Metal Complexes ESI of Surfactants Oligonucleotides, DNA, and RNA ESI of Oligosaccharides Atmospheric Pressure Chemical Ionization Atmospheric Pressure Photoionization General Characteristics of ESI Sample Consumption Types of Ions in ESI Mass Analyzers for ESI Reference List Hyphenated Methods General Properties of Chromatography-Mass Spectrometry Coupling Chromatograms and Spectra Selected Ion Monitoring Quantitation Gas Chromatography-Mass Spectrometry GC-MS Interfaces Volatility and Derivatization Column Bleed Fast GC-MS Liquid Chromatography-Mass Spectrometry LC-MS Interfaces Multiplexed Electrospray Inlet Systems Tandem Mass Spectrometry Ultrahigh-Resolution Mass Spectrometry Reference List

16 XVIII Table of Contents Appendix Isotopic Composition of the Elements Carbon Isotopic Patterns Silicon and Sulfur Isotopic Patterns Chlorine and Bromine Isotopic Patterns Characteristic Ions Frequent Impurities Subject Index