Title Details

Marek Smoluch, PhD, is an associate professor in the Department of Biochemistry and Neurobiology at AGH University of Science and Technology, Krakow, Poland.

Giuseppe Grasso, PhD, is an associate professor in the Department of Chemical Sciences at the University of Catania, Catania, Italy.

Piotr Suder, PhD, is an associate professor in the Department of Biochemistry and Neurobiology at AGH University of Science and Technology, Krakow, Poland.

Jerzy Silberring, PhD, is a professor and the Head of the Department of Biochemistry and Neurobiology at AGH University of Science and Technology, Krakow, Poland.

List of Contributors

Preface

I. Introduction

II. Brief history of mass spectrometry

III. Basic definitions

IV. Instrumentation

IV.1. Ionization methods

IV.1.1. Electron Impact (EI)

IV.1.2. Chemical ionization (CI)

IV.1.3. Atmospheric pressure ionization (API)

IV.1.3.01 Atmospheric pressure chemical ionization (APCI)

IV.1.3.02 Electrospray (ESI)

IV.1.3.02.1 Introduction

IV.1.3.02.2 ESI principle of operation

IV.1.3.02.3 ESI – working principles

IV.1.3.02.4 Properties of the solvent

IV.1.3.02.5 Principles of ESI-MS spectra interpretation

IV.1.3.03 Nanoelectrospray (nanoESI)

IV.1.3.03.1 Introduction

IV.1.3.03.2 Nanospray sensitivity

IV.1.3.03.3 Ionization in nanoelectrospray and electrospray ion sources

IV.1.3.03.4 Off-line nanospray and practical advices

IV.1.3.03.5 On-line nanospray and practical advices

IV.1.3.03.6 Summary

IV.1.3.04 Desorption electrospray ionization (DESI)

IV.1.3.04.1 Introduction

IV.1.3.04.2 Construction of the ion source

IV.1.3.04.3 Principles of operation

IV.1.3.04.4 Mechanism of ions formation

IV.1.3.04.5 The role of surface for sample deposition

IV.1.3.04.6 Reactive DESI

IV.1.3.05 Laser ablation electrospray ionization (LAESI)

IV.1.3.06 Photoionization

IV.1.4. Ambient plasma based ionization techniques

IV.1.4.01 Introduction

IV.1.4.02 Direct analysis in real time (DART)

IV.1.4.02.1 Introduction

IV.1.4.02.2 Construction of the ion source

IV.1.4.02.3 Mechanism of ions generation

IV.1.4.02.4 Applications of DART

IV.1.4.02.5 Coupling with chromatographic techniques

IV.1.4.03 Flowing atmospheric pressure afterglow (FAPA)

IV.1.4.03.1 Introduction

IV.1.4.03.2 Construction of the ion source

IV.1.4.03.3 Mechanism of ionization

IV.1.4.03.4 Applications of FAPA

IV.1.4.03.5 Coupling with other techniques

IV.1.4.04 Dielectric Barrier Discharge Ionization (DBDI)

IV.1.4.04.1 Introduction

IV.1.4.04.2 Construction of the ion source

IV.1.4.04.3 Mechanism of ionization

IV.1.4.04.4 Applications of DBDI

IV.1.5 Matrix assisted laser desorption/ionization (MALDI)

IV.1.5.01 Introduction

IV.1.5.02 The role of matrix

IV.1.5.03 Atmospheric pressure MALDI

IV.1.5.04 MALDI mass spectra interpretation

IV.1.5.05 Ionization/desorption on porous silicon (DIOS)

IV.1.5.06 Surface enhanced laser desorption/ionization (SELDI)

IV.1.5.07 Nanostructure enhanced laser desorption/ionization (NALDI)

IV.1.5.08 Summary

IV.1.6 Inductively coupled plasma ionization (ICP)

IV.1.6.01 Introduction

IV.1.6.02 ICP as a technique of elemental analysis and ICP principle

IV.1.6.03 Ionization of elements and ionization efficiency

IV.1.6.04 Mechanism of inductively coupled ICP formation

IV.1.6.05 Ways of plasma view and plasma generation

IV.1.6.06 Sample introduction

IV.1.6.07 Measurement in the ICP-MS technique

IV.1.6.08 Analyzers in ICP-MS spectrometers

IV.1.7 Secondary ion mass spectrometry with Time-of-Flight analyser (TOF-SIMS)

IV.1.7.01 Introduction

IV.1.7.02 TOF-SIMS principle of operation

IV.1.7.03 The sputtering of the sample surface

IV.1.7.04 Ionization (generating secondary ions)

IV.1.7.05 Construction of TOF-SIMS

IV.1.7.06 Analytical capabilities of TOF-SIMS

IV.1.7.06.1 Static TOF-SIMS

IV.1.7.06.2 Visualization of sample surface

IV.1.7.06.3 Dynamic SIMS – in-depth analysis

 IV.1.7.07 Examples and spectra interpretation

IV.1.7.07.1 Speciation analysis

IV.1.7.07.2 Distribution of species on the surface

IV.1.7.07.3 In-depth speciation analysis

IV.2 Analyzers

IV.2.1. Time-of-Flight (TOF)

IV.2.1.01 Introduction

IV.2.1.02 The working rule of TOF analyzer

IV.2.1.03 Linear mode of operation of TOF

IV.2.1.04 The spread of the kinetic energy regarding the ions of the same mass

IV.2.1.05 Delayed ion extraction

IV.2.1.06 The reflection mode

IV.2.1.07 Orthogonal acceleration

IV.2.1.08 Summary

IV.2.2. Ion mobility analyzer (IM)

IV.2.2.01 Principle of IM operation

IV.2.2.02 Drift time IMS

IV.2.2.03 FAIMS (high-field asymmetric waveform ion mobility spectrometer)

IV.2.2.04 TWIG (travelling wave ion guides)

IV.2.2.05 IM spectrum

IV.2.2.06 Applications

IV.2.3 Quadrupole mass analyzer (Q)

IV.2.3.01 Construction and principles of operation of a quadrupole

IV.2.3.02 Behavior of an ion inside the quadrupole

IV.2.3.03 How mass spectrum is generated? Changes of U and V

IV.2.3.04 Spectrum quality

IV.2.3.05 Applications of the quadrupole analyzer

IV.2.3.06 Quadrupoles, hexapoles and octapoles as focusing elements - ion guides

IV.2.4. Ion trap (IT)

IV.2.4.01 Introduction

IV.2.4.02 Behavior of an ion inside the ion trap

IV.2.4.03 Analysis of the ions

IV.2.4.04

Tandem in space

Mass Selective Instability Mode

IV.2.4.05 Resonant Ejection Mode

IV.2.4.06 Axial Modulation

IV.2.4.07 Nonlinear Resonance

IV.2.4.08 Linear ion trap LIT

IV.2.4.09 Applications

IV.2.5. High resolution mass spectrometry

IV.2.5.01 Introduction

IV.2.6. Ion cyclotron resonance (ICR)

IV.2.6.01 Introduction

IV.2.6.02 Cyclotron frequency

IV.2.6.03 ICR - principles of operation

IV.2.6.04 Injection of ions into the ICR cell

IV.2.6.05 Trapping electrodes

IV.2.6.06 Excitation electrodes

IV.2.6.07 Detection electrodes and Fourier transform

IV.2.6.08 FT-ICR properties as m/z analyzer

IV.2.7. Orbitrap

IV.2.7.01 History of development, principles of operation

IV.2.7.02 Analyzing ions in the orbitrap

IV.2.7.03 Orbitrap properties as m/z analyzer

IV.2.7.04 Analytical and proteomic applications of Orbitrap

IV.2.8. Hybrid instruments

IV.2.8.01 A brief comparison of mass analyzers

IV.2.8.02 Triple quadrupoles

IV.2.8.03 Q-IT

IV.2.8.04 Q-Orbitrap

IV.2.8.05 Q-TOF

IV.2.8.06 IT-TOF

IV.2.8.07 IT-Orbitrap

IV.2.9. Sector instruments

 IV.2.9.01 Introduction

IV.2.9.02 Rule of operation of magnetic analyzer (B)

IV.2.9.03 Electrostatic sector (E)

IV.2.9.03 Mass spectrometer with magnetic and electrostatic sector

IV.3. Ion detectors

IV.3.1. Introduction

IV.3.2 Electron multiplier

IV.3.3. Microchannel detector

IV.3.4. Medipix/Timepix detectors

IV.3.5. Ion detection in ICR and orbitrap based mass spectrometers

V. Hyphenated techniques

V.1. Gas chromatography combined with mass spectrometry GC-MS

V.1.1. Introduction

V.1.2 Detectors

V.1.3. Chemical modifications – derivatization

V.1.4. GC-MS analysis

V.1.5. Two-dimensional gas chromatography linked to mass spectrometry 2D GC-MS

V.2. Liquid chromatography linked to mass spectrometry (LC-MS)

V.2.1. Introduction

V.2.2. Introduction to liquid chromatography

V.2.3. Types of detectors

V.2.4. Chromatographic columns

V.2.5. Chromatographic separation and quantitation using MS as a detector

V.2.6. Construction of an interface linking liquid chromatograph to the mass spectrometer

V.2.6.01 Introduction

V.2.6.02 ESI interface

V.2.6.03 APCI connection to MS

V.2.6.04 APPI interface

V.2.6.05 LC connection to MALDI-MS

V.2.6.06 Multidimensional separations

V.3. Capillary electrophoresis linked to mass spectrometry

V.3.1 Introduction

V.3.2. Types of electrophoretic techniques

V.3.3. Capillary electrophoresis linked to ESI

V.3.3.01 Liquid sheath connection

V.3.3.02 Sheath-free connection

V.3.3.03 Liquid junction

V.3.4. Capillary electrophoresis linked to matrix assisted laser desorption/ionization

V.3.4.01 Off-line CE-MALDI-TOF

V.3.4.02 Direct CE-MALDI-TOF

V.3.4.03 On-line CE-MALDI-TOF

V.3.5. Summary

VI. Mass spectrometry imaging (MSI)

VI.1 Introduction

VI.2 SIMS

VI.3 MALDI-IMS

VI.4 DESI

VI.5 Analysis of tissue sections using MSI techniques

VI.6 Analysis of individual cells and cell cultures using MSI techniques

VI.7 Analysis with MSI techniques – examples

VI.8 Combinations of different imaging techniques

VI.9 Summary

VII. Tandem mass spectrometry

VII.1 Introduction

VII.2 Principles

VII.3 Strategies for MS/MS experiments

VII.3.1 Tandem in space

VII.3.2 Tandem in time

VII.3.3 Multiple fragmentation

VII.4. Fragmentation techniques

VII.4.1 Introduction

VII.4.2 (low energy) Collision-induced dissociation (CID)

VII.4.3 High energy collisional dissociation (HCD)

VII.4.4 Pulsed Q collision induced dissociation PQD

VII.4.5 Electron capture dissociation (ECD)

VII.4.6 Electron transfer dissociation (ETD)

VII.4.7 Electron detachment dissociation (EDD)

VII.4.8 Negative electron-transfer dissociation (NETD)

VII.4.9 Infrared multiphoton dissociation (IRMPD)

VII.4.10 Blackbody infrared radiative dissociation (BIRD)

VII.4.11 Post-source decay (PSD), metastable ions detection

VII.4.12 Surface-induced dissociation (SID)

VII.4.13 Charge remote fragmentation

VII.4.14 Chemically activated fragmentation (CAF)

VII.4.15 Proton transfer reaction (PTR)

VII.5. Practical aspects of fragmentation in mass spectrometers

VII.5.1 In-source fragmentation

VII.5.2 Triple quadrupole fragmentation

VII.5.3 Ion traps

VII.5.4 Time-of-Flight analyzers

VII.5.5 Combined time of flight analyzers (TOF-TOF)

VII.5.6 Hybrid instruments

VII.5.7 Mass spectrometers equipped with orbitrap analyzer

VII.6. Applications of tandem mass spectrometry in life sciences

VII.7. SWATH fragmentation

VIII. Mass spectrometry applications

VIII.1. Mass spectrometry in proteomics

VIII.1.1 Introduction

VIII.1.2 Bottom-up vs. Top-down proteomics

VIII.1.2.01 Bottom-up proteomics

VIII.1.2.02 Top-down proteomics

VIII.1.3 Database search and protein identification

VIII.1.4 In-deep structural characterization of a single protein: an example

VIII.1.5 Quantitative analysis in proteomics

VIII.1.5.01 Introduction

VIII.1.5.02 iTRAQ (isobaric tags for relative and absolute quantitation)

VIII.1.5.03 ICAT (isotope coded affinity tagging)

VIII.1.5.04 SILAC (stable isotope labeling in culture)

VIII.1.5.05 SILAM (stable isotope labeling of mammals)

VIII.1.5.06 MCAT (mass coded abundance tagging)

VIII.1.5.07 Label free techniques

VIII.2. Food Proteomics

VIII.3. Challenges in analysis of OMICS data generated by mass spectrometry

VIII.3.1 Introduction

VIII.3.1.01 How big must Big Data be?

VIII.3.1.02 Do omics platforms generate unstructured data?

VIII.3. 2 Targeted and full unbiased omics analysis based on mass spectrometry technology

VIII.3.2.01 Factors affecting data quality

VIII.3.2.02 Speed of MS data acquisition: Why does it matter?

VIII.3.2.03 Analytical strategies in omics studies

VIII.3.3 Data analysis and visualization of mass spectrometry OMICS data

VIII.3.3.01 A brief introduction to data visualization

VIII.3.3.02 Exploration and preparation of data for downstream statistics and visualization

VIII.3.3.02.1 Data Organization

VIII.3.3.02.2 Principal Component Analysis (PCA)

VIII.3.3.02.3 Transformation and Normalization

VIII.3.3.03 Differential expression analysis

VIII.3.3.03.1 Visualizing results

VIII.3.3.04 Strategies for visualization beyond three dimensions

VIII.3.3.05 Bioinformatics tools

VIII.3.4 Databases and search algorithms

VIII.3.4.01 Databases for proteomics.

VIII.3.4.01.1 Search engines for proteomics

VIII.3.4.02 Databases for metabolomics

VIII.3.5 Validation of high throughput data - current challenges

VIII.3.5.01 Analytical validation

VIII.3.5.02 Statistical validation

VIII.3.5.03 Bioinformatic validation

VIII.3.6 Summary and conclusions

VIII.4 Application of the mass spectrometric techniques in the earth sciences

VIII.4.1 Introduction

VIII.4.2 Conventional geochronology

VIII.4.3 In situ geochronology

VIII.4.4 Geochemical and isotopic tracing

VIII.5 Mass spectrometry in space

VIII.6 Mass spectrometry in the study of art and archaeological objects

VIII.6.1 Introduction

VIII.6.2 MS-methods for the study of inorganic components of art and archaeological objects

VIII.6.3 MS-methods for the study of organic components of art and archaeological objects

VIII.7 Application of ICP-MS for trace elemental and speciation analysis

VIII.7.1 Introduction

VIII.7.2 Speciation analysis by ICP-MS – examples of applications

VIII.7.3 Single particle and single cell analysis by ICP-MS – examples of applications

VIII.7.4 Imaging by LA-ICP-MS technique

VIII.7.5 Improvements of LA-ICP-MS technique

VIII.7.6 LA-ICP mass spectrometer with LIBS

VIII.8 Mass spectrometry in forensic research

VIII.9 Doping in sport

VIII.10 Miniaturization in mass spectrometry

IX. Appendix

IX.1. Pressure units

IX.2. Most commonly detected fragments generated by Electron Impact ionization (EI)

IX.3. Trypsin autolysis products

IX.4. Proteolytic enzymes for proteins identification

IX.5. Molecular masses and amino acid residues

IX.6. Molecular masses of less common amino acid residues

IX.7. Important www addresses

IX.8. Internet data bases

IX.8.1 References

IX.8.2 Bioinformatics tools

X. Abbreviations

XI. Index