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Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation, 4th Edition

Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation, 4th Edition

J. Throck Watson, O. David Sparkman

ISBN: 978-1-118-68158-9

Jul 2013

864 pages



Completely revised and updated, this text provides an easy-to-read guide to the concept of mass spectrometry and demonstrates its potential and limitations. Written by internationally recognised experts and utilising "real life" examples of analyses and applications, the book presents real cases of qualitative and quantitative applications of mass spectrometry. Unlike other mass spectrometry texts, this comprehensive reference provides systematic descriptions of the various types of mass analysers and ionisation, along with corresponding strategies for interpretation of data. The book concludes with a comprehensive 3000 references.

This multi-disciplined text covers the fundamentals as well as recent advance in this topic, providing need-to-know information for researchers in many disciplines including pharmaceutical, environmental and biomedical analysis who are utilizing mass spectrometry

Chapter 1: Introduction.

I. What is Mass Spectrometry.

II. History.

III. Applications.

IV. The Data of Mass Spectrometry and Its Presentation.

1. Spectra.

2. Total Ion Current.

3. Mass Chromatograms and Profiles.

V. Definition of Terms.

1. Mass-To-Charge Ratio (m/z).

2. Multiple-Charge Ions.

3. Ions Representing an Intact Molecule.

4. Resolution/Resolving Power.

5. Intensity vs Abundance.

Chapter 2: The Mass Spectrometer.

I. Introduction.

II. Ion Guides.

III. Types of m/z Analyzers.

1. Time-Of-Flight.

A. Linear.

1) Resolving Power of the Linear TOF Instrument.

2) Time-Lag Focusing.

3) Beam Deflection.

B. Reflectron.

C. Orthogonal Acceleration.

D. Ion Detection in the TOF Analyzer.

1) Time Slice Detection.

2) Time Array Detection.

3) TAD with Transient Recorders.

4) TAD with an Integrating Transient Recorder.

5) Hadamard Transform TOF MS.

2. Quadrupole Ion Traps.

A. 3D Quadrupole Ion Traps.

B. Linear Quadrupole Ion Traps.

3. Orbitrap.

A. Historical Aspects.

B. Operating Principles.

4. Transmission Quadrupoles.

A. QMF Equations of Motion.

B. The Stability Diagram.

C. Characteristics of Output.

D. Spectral Skewing.

E. Performance Limitations.

5. Sector instruments.

A. Single-focusing Instruments.

1) Operating Principles.

2) Performance Limitations.

B. Double-Focusing Instruments.


C. Hardware Configuration.

D. Operational Considerations.

E. Representative Applications.

IV. Calibration of the m/z Scale.

1. Electron Ionizaton (GC/MS).

2. Chemical Ionization (GC/MS).

3. Electrospray and Other Atmospheric Pressure Ionization Techniques.

V. Ion Detection.

1. General Considerations.

2. Types of Detectors.

A. Faraday Cup.

B. Electron Multiplier.

1) Discrete-Dynode Version.

2) Continuous-Dynode Version.

C. Negative-Ion Detection.

D. Post-Acceleration Detection and Detection of High-Mass Ions.

E. Channel Electron Multiplier Array (CEMA).

F. Electro-Optical Ion Detection.

G. The Daly Detector.

H. Cryogenic Detectors.

VI. Vacuum Systems.

1. Introduction.

2. Definitions.

3. Pressure Gauges.

A. Thermal-Conductivity Gauges.

B. Ionization Gauges.

4. Types of Pumps.

A. Mechanical Pumps (Low Vacuum).

1) Rotary Vane.

2) Scroll.

3) Diaphram.

B. High Vacuum.

1) Turbomolecular Pumps.

2) Diffusion Pumps.

3) Sputter-Ion Pumps.

4) Cryogenic Pumps.

Chapter 3: Mass Spectrometry/Mass Spectrometry.

I. Introduction.

1. Concept and Definitions.

2. Nomenclature.

II. Ion Dissociation.

1. Metastable Ions.

III. Instrumentation for MS/MS.

1. MS/MS in Space.

A. Tandem MS/MS.

1) Triple-Quadrupole Mass Spectrometer.

2) BEqQ Hybrid Instrument.

B. Double-Focusing Instruments.

2. MS/MS in Time.

IV. Specialized Techniques and Applications.

1. In-Source CAD.

2. CAD in Conjunction with Soft Ionization.

3. Selected Reaction Monitoring.

4. Precursor-Ion Scan.

5. Neutral Loss (Common Loss) Scan.

6. Ion/Molecule Reactions.

V. Identification of Unknowns from CAD Data.

1. Accurate Mass Measurements.

2. Library Search Utilities.

A. Other Databases.

B. Substructure Information.

C. Use of MS Interpreter.

Chapter 4: Inlet Systems.

I. Introduction.

II. Batch Inlets.

1. Heated Reservoir Inlet.

2. Direct Inlet Probe (DIP).

A. The Chromatoprobe.

3. Direct Exposure Probe (Desorption Chemical Ionization [DCI]).

4. Pyrolysis.

III. Continuous Inlets.

1. Membrane Introduction MS (MIMS).

2. Supercritical Fluid Chromatography.

3. Electrophoretic Inlet.

IV. Ionization Inlet Systems.

1. Direct Analysis in Real Time (DART).

2. Desorption Electrospray Ionization (DESI).

3. Desorption Atmospheric Pressure Chemical Ionization (DAPCI).

V. 4. Speciality Interfaces.

1. Selected Ion Flow-Tube Mass Spectrometry (SIFT-MS).

2. Fast Atom Bombardment (FAB) and Liquid Secondary Ion Mass Spectrometry (LSIMS).

3. Chemical Reaction Interface Mass Spectrometry (CRIMS).

4. ICP.

Chapter 5: Strategies for Data Interpretation (Other than Fragmentation).

I. Introduction.

II. Some Important Definitions.

III. The Possible Information That Can be Obtained from the Mass Spectrum.

IV. Elemental Composition of an Ion and the Ratios of Its Isotope Peaks.

1. Definition of Terms Related to the Matter of Mass Spectrometry.

2. Nitrogen Rule.

3. Elemental Composition of an Ion Based on Intensities of Isotope Peaks.

B. Use of Isotope Peaks Intensities to Determine the Elemental Composition of Ions.

C. Isotope Peaks Patterns for Ions Containing Various Combinations of Cl and/or Br.

D. Constraints on the Number of Atoms of a Given Element.

E. Relationship between the Spacing of Isotope Peaks and the Charge State of an Ion.

3) Ions of Low-Charge State.

4) Ions of High-Charge State.

F. Steps to Assigning an Elemental Composition Based on Isotope Peaks Intensities.

G. Validating the Putative Elemental Composition of an Ion.

H. Some Illustrative Examples.

I. Potential Problems Arising from Adjacent Peaks.

4. Accurate Mass Measurements.

A. Appearance of Mass Spectra of High-m/z Value Ions.

5. Use of the NIST Mass Spectral Search Program in the Determination of a Structure from an Elemental Composition.

6. Does the Result Make Sense?

V. Identifying the Molecular Mass of an Analyte.

1. Identification of a Molecular-Ion Peak.

2. Identification of a Protonated-Molecule Peak.

A. The Role of Adduct-Ion Peaks.

3. Recognition of the Deprotonated Molecule ([M - H] - ) Peak in Soft Ionization.

VI. Recognition of Spurious Peaks in the Mass Spectrum.

1. Noise Spikes.

2. Peaks Corresponding to Contaminants in GC/MS and LC/MS.

A. Phthalate Ion.

B. GC Column Bleed.

C. Solvent Clusters.

VII. Obtaining Structural Information from Mass Spectra.

Chapter 6: Electron Ionization.

I. Introduction.

II. Ionization Process.

III. Strategy for Data Interpretation.

1. Assumptions.

2. The Ionization Process.

IV. Types of Fragmentation Pathways.

1. Sigma-Bond Cleavage.

2. Homolytic Cleavage.

3. Heterolytic Cleavage.

4. Rearrangements.

A. Hydrogen Shift Rearrangements.

B. Hydride Shift Rearrangements.

V. Representative Fragmentations (Spectra) of Classes of Compound.

1. Hydrocarbons.

A. Saturated Hydrocarbons.

1) Straight Chain.

2) Branched.

3) Cyclic.

B. Unsaturated.

C. Aromatic.

2. Alkyl Halides.

3. Oxygen-Containing Compounds.

A. Aliphatic Alcohols.

B. Aliphatic Ethers.

C. Aromatic Alcohol.

D. Cylic Ethers.

E. Ketones and Aldehydes.

F. Esters and Acids.

1) Aliphatic.

2) Aromatic.

4. Nitrogen-Containing Compounds.

A. Aliphatic Amines.

B. Aromatic Compounds with Nitrogen Atoms.

C. Heterocyclic Nitrogen Compounds.

D. Nitro Compound.

E. Concluding Remarks on Nitrogen Containing Compounds.

5. Multiple Heteroatoms or Heteroatoms and Double Bonds.

6. Trimethylsilyl Derivatives.

7. Determining the Location of Double Bonds.

VI. Library Search.

1. Databases.

2. Library Search Programs.

3. What to Do When the Spectrum of the Unknown Is Not In the Database(s).

4. Searching Multiple Databases.

5. Database Size and Quality.

6. Concluding Remarks on the NIST Mass Spectral Search Program.

VII. Summary of Interpretation of EI Mass Spectra.

Chapter 7: Chemical Ionization.

I. Introduction.

II. Description of the Chemical Ionization Source.

III. Production of Reagent Ions from Various Reagent Gases.

IV. Positive-Ion Formation Under CI.

1. Fundamentals.

2. Practical Consideration of Proton Affinity.

3. Selective Ionization.

4. Fragmentation.

V. Negative-Ion Formation under CI.

VI. Data Interpretation and Systematic Studies of CI.

VII. Ionization by Charge Exchange.

1. Mechanism of Ionization.

2. Fragmentation and Appearance of Mass Spectra.

IX. Desorption Chemical Ionization .

X. General Applications.

Chapter 8: Electrospray Ionization.

I. Introduction.

II. Operating Principles.

III. Appearance of ESI Mass Spectra and Data Interpretation.

IV. ESI with High Mass Resolving Power.

V. Implementations of Electrospray.

1. Conventional ESI Source Interface.

2. Nanospray and Microspray.

3. Desorption Electrospray Ionization (DESI).

VI. Effect of Composition and Flowrate of Analyte Solution.

VII. Special Applications.

1. Direct Analysis of Ions in Solution by ESI.

2. Cold Spray Ionization.

3. Negative Ion Detection.

4. Secondary Electrospray Ionization.

5. Kinetic Measurements of Chemical Reactions.

VIII. General Applications.

Chapter 9: MALDI.

I. Historical Perspective and Introduction.

II. Operating Principles.

1. The Matrix.

2. The Laser and m/z Analyzer.

3. The Ionization Process.

4. Atmospheric-Pressure MALDI.

III. Sample Handling.

1. Sample Preparation of the Conventional Plate.

2. The Problem of Analyte Solubility.

3. The Problem of Sample Purity.

4. On-Probe Sample-Cleaning Techniques.

A. SAMs and Polymer-Modified Surfaces

B. Affinity Surfaces.

5. Direct Analysis from Gels.

6. Hydrogen/Deuterium Exchange.

IV. Special Instrumental Techniques.

1. Post-Source Decay (PSD).

2. Ion Excitation.

3. Delayed Extraction (DE).

4. Desorption Ionization On Silicon (DIOS).

5. Tissue Profiling.

V. Representative Applications.

1. Peptides and Proteins.

2. Microbes.

3. Biomarkers.

4. Synthetic Polymers.

5. Small Molecules.

6. Quantitation.

7. Combined with Liquid Chromatography.

Chapter 10: GC/MS.


I. Introduction to GC.

1. Basic Types of Injection.

2. Injection Considerations and Syringe Handling.

II. Sample Handling.

III. Instrument Requirements for GC/MS.

1. Operating Pressures.

2. Typical Parameters for a GC-MS Interface.

3. Open-Split Interface.

4. Separators.

C. Jet-Orifice Separator.

D. Membrane Separator.

5. Inertness of Materials in the Interface.

6. Background/Bleed.

7. Qualitative vs Quantitative Assessment of GC/MS Data.

IV. Operational Considerations.

1. Spectral Skewing.

2. Rapid Scanning.

3. Fast Chromatography.

A. Status Quo.

B. Performance Trade-Offs of Conventional Instruments for GC/MS.

C. Time Array Detection.

4. Selected Ion Monitoring (SIM).

A. Definitions/Nomenclature.

B. Development of the Technique.

C. Introductory Qualitative Example.

D. Introductory Quantitative Example.

E. Mechanics of Ion Monitoring.

F. Programmable SIM.

G. SIM at High Resolving Power.

V. Sources of Error.

VI. Representative Applications of GC/MS.

Chapter 11: Liquid Chromatography/Mass Spectrometry.

I. Introduction.

II. Historical Milestones in the Development of the Interface.

1. Direct Inlet.

2. Moving Belt Interface.

3. Thermospray Interface.

4. Continuous Flow FAB.

III. Currently Viable Versions of the Interface.

1. Atmospheric-Pressure Ionization.

A. Electrospray Interface.

1 Optimization for Analyses by HPLC.

2) Data-Dependent Analysis.

3) Capillary Electrophoresis.



2. Particle Beam Interface.

3. EI.

IV. Operational Considerations (Special Operation of LC under MS Conditions).

1. Solvents .

2. Buffers.

3. Columns.

4. etc.

V. Applications.

Chapter 12: Analysis of Proteins and other Biopolymers.

I. Proteins.

1. Sequencing.

A. Nomenclature and Fragmentation in Sequencing of Peptides.

B. Strategy for Deducing Amino Acid Sequence via CAD of Peptides.

1) An Illustrative Example.

2) Possible Pitfalls in Interpretation.

3) Search for Confirming Ions.

4) Ladder Sequencing.

2. Mass Mapping.

3. Posttranslational Modifications.

A. Phosphorylation.

1) An Illustrative Example.

2) Selective Capture and Detection of Phosphopeptides.

3) Chemical Modification of Phosphorylation Sites.

B. Recognition of Sites of Sulfation.

C. Recognition of Sites of Glycosylation.

D. Acetylation of Lysine.

E. Cysteine Status.

1) Are There Any Disulfide Bonds?

2) Which Cysteines Are Free?

3) What is the Linkage of Cysteines in Disulfide Bonds?

(a) Conventional Proteolytic Mass Mapping of Disulfides.

(b) Cyanlation-Based Mass Mapping of Disulfides.

4) Recognition of Ubiquinated Proteins.

4. Quantitation in Proteomics.


5) Operating Principles.

6) Illustrative Example of the ICAT Approach.

7) Analogous Developing Methodologies.

B. Alternative Stable-Isotope Labeling Methodology.

5. "Top-Down" Strategies of Analysis.

1) Instrumentation and Fragmentation Requirements.

2) Electron Capture Dissociation (ECD).

3) Electron Transfer Dissociation (ETD).

6. Non-Covalent Interactions.

7. Folding and Unfolding.

8. Applications.

II. Oligonucleotides.

1. Analytical Considerations.

2. Sequencing.

A. Nomenclature.

B. Algorithm for Data Interpretation.

3. Applications.

III. Carbohydrates.

1. Analytical Considerations.

2. Nomenclature.

3. Diagnostic Fragmentation.

4. Applications.

  • A chapter on the analysis of Proteins and Biopolymers
  • Strategies for interpretation of all mass spectral data (EI, soft ionization, MS/MS, etc.)
  • Use of many of the data handling programs that have evolved over the last 10 years
  • New instrumentation such as the linear QIT, Orbitrap, tandem instruments incorporating ion mobility spectrometry, etc.
  • Advances in pumping and detector technology
  • Expanded study of the interpretation of EI mass spectra
  • History and evolution of mass spectrometry
  • More in-depth information on the "how" of LC/MS as well as the traditional that was found in the previous edition and most current text on mass spectrometry
  • New MS/MS technologies in ion traps such as ECD and ETD
"The writing here is approachable, honest and understandable. One gets the sense that a very knowledgeable friend is sharing the story of mass spectrometry with you.... This hefty single volume is a mature presentation of all major topics in organic and biological mass spectrometry." (Journal of Chemical Education, July 2009)

  “Introduction to Mass Spectrometry, Instrumentation, Applications, and Strategies for Data Interpretation definitely adds to the selection of general mass spectrometry textbooks in a valuable manner. It is capable of delivering introductory-level knowledge for the undergraduate as well as of providing detailed information for those getting into mass spectrometry.” (Analytical Science and Bioanalytical Chemistry, July 2008)

"An easy-to-read guide to the concept of mass spectrometry, and demonstrates its potential and limitations....   This comprehensive reference provides systematic descriptions of the various types of mass analyzers and ionization, along with corresponding strategies for interpretation of data." (MP Materials Testing, February 2009)

"An easy-to-read guide to the concepts of mass spectrometry, its potential, and its limitations." (Materials and Corrosion, November 2007)

"This book should certainly be on the bookshelf of every mass spectrometrist." (International Journal of Environmental and Analytical Chemistry, 2008)

"The book is a very useful reference, and will be a useful work for teaching mass spectrometry." (CHOICE, April 2008)

"Provides an easy to read guide…this comprehensive reference provides systematic descriptions…This latest edition provides students with a complete overview of principles.” (Materials Evaluation, December 2007)

"This completely updated text provides an easy-to-read guide to the concepts of mass spectrometry, its potential, and its limitations." (Materials and Corrosion, November 2007)

  • Covers a mainstream topic for all mass spectrometrists in all application areas
  • Utilizes "real life" examples of analyses and applications
  • Presents real cases of qualitative and quantitative applications of mass spectrometry
  • Concludes with a comprehensive list of approximately 3,000 references
  • Includes Instructor's Support files, which can be accessed at