List of Contributors xvii Section I Basics and Fundamentals 1 1 Definitions and Concepts for Targeted and Nontargeted Chemical Analysis 3 Marco De Poli, Allan Polidoro, and Flavio A. Franchina 1.1 Introduction 3 1.2 Conceptual Foundations 4 1.2.1 Analytical Strategies 4 1.2.2 Resolution 8 1.
2.2.1 Chromatographic Resolution 8 1.2.2.2 Mass Spectrometric Resolution 9 1.3 Analytical Information Continuity 10 1.3.
1 Sample Preparation as an Information Filter 11 1.3.2 Sample Introduction as a Selective Interface 13 1.3.3 Chromatographic Separation 13 1.3.4 Mass Spectrometry and Informational Depth 14 1.3.
5 Data Governance 15 1.3.6 Cumulative Effects Across the Analytical Workflow 16 References 17 2 GC-Suited Sample Preparation Approaches for Omics Studies 21 Flavio A. Franchina, Damien Pierret, and Giorgia Purcaro 2.1 Introduction 21 2.2 Sampling Techniques for Volatile Analyte Analysis 23 2.2.1 Static and High-capacity Headspace Analysis 23 2.
2.2 Dynamic Headspace Sampling 30 2.3 Analysis of Semivolatiles Analytes 32 2.3.1 Liquid-phase-based Sampling Techniques 34 2.3.1.1 Microextractions 34 2.
3.1.2 Assisted Techniques 36 2.3.2 Solid-Phase-Based Sampling Techniques 37 2.3.3 Chemical Transformations (Derivatization) 38 References 41 3 Principles of High-resolution GC and GC×GC 51 Peter Q. Tranchida, Micaela Galletta, and Luigi Mondello 3.
1 Introduction 51 3.2 High-resolution GC 52 3.3 Multidimensional GC 56 3.3.1 Comprehensive 2D GC 56 3.3.1.1 The Invention and Principles 56 3.
3.2 Modulation Approaches 60 3.3.2.1 Thermal Modulation 60 3.3.2.2 Flow Modulation 61 3.
3.3 Method Optimization 64 3.3.3.1 Stationary Phase Selection 64 3.3.3.2 Column Dimensions and Gas Flow(s) 66 3.
3.3.3 Modulation 69 3.3.4 Detection 70 References 73 4 Basic Principles of Mass Spectrometry 79 Nadine Gawlitta, Barbara Giocastro, Thomas Gröger, Beate Gruber, Christopher Rüger, Benedikt Weggler, and Ralf Zimmermann 4.1 Key Concepts and Definitions 79 4.1.1 Getting Started 79 4.
1.2 The Mass Spectrum and Some Definitions 80 4.1.3 Resolution, Resolving Power, and Accurate Mass 82 4.1.4 Chromatographic Hyphenation 83 4.2 Working Principles and Instrumentation 83 4.2.
1 The Gas Phase Interface 84 4.2.1.1 Carrier Gas Consideration 86 4.2.2 Principle of Ion Formation and Ionization Techniques 87 4.2.2.
1 Electron Ionization 88 4.2.2.2 Chemical Ionization 90 4.2.2.3 Photo Ionization 92 4.2.
2.4 Proton Transfer Reaction Ionization 95 4.2.3 The Mass Analyser 95 4.2.3.1 Quadrupole Mass Analyser 96 4.2.
3.2 Triple Quadrupole Mass Analyser 99 4.2.3.3 Time-of-flight Mass Analyser 102 4.2.3.4 Quadrupole Time-of-flight Hybrid Mass Analyzer 105 4.
2.3.5 Orbitrap Mass Analyzer 109 4.2.3.6 Ion Mobility Hyphenation 112 4.2.3.
7 Mass Calibration 114 4.2.4 Ion Detection and Detectors 115 4.2.4.1 Faraday Cup 115 4.2.4.
2 Secondary Electron Multipliers and Channel Electron Multiplier 116 4.2.4.3 Microchannel Plates 116 4.2.4.4 Photomultipliers 117 4.2.
4.5 Conversion Dynodes 117 4.2.5 Electronic Signal Processing 117 4.3 MS Data and Basic Data Handling 118 4.3.1 Deconvolution of (GC-)MS Signals 119 4.3.
2 The Qualitative Information 120 4.3.2.1 Interpretation of the Fragmentation Pattern 121 4.3.2.2 Scripting and Filtering 123 4.3.
2.3 Mass Spectra Libraries 123 4.3.2.4 Seven Golden Rules 124 4.3.2.5 The High Resolution Advantage 125 4.
3.2.6 Data Visualisation of Exact Accurate Data 127 4.3.3 The Quantitative Information 128 4.3.3.1 Quantification 128 4.
3.3.2 Isotopic Labelling 130 References 131 5 Management and Interpretation of GC and MS Detailed Data 139 Glaucimar A. P. de Resende, Allyson L. R. dos Santos, and Leandro W. Hantao 5.
1 Fundaments 139 5.2 GC-MS Applications 142 5.3 GC×GC-MS Applications 145 5.4 Data Treatment 153 5.4.1 Pretreatment 155 5.4.2 Model Construction 162 5.
4.3 Univariate Strategies 166 5.4.4 Pattern Recognition 176 5.4.5 Curve Resolution/Deconvolution 179 5.4.6 Regression 183 5.
4.7 Classification/Discrimination 185 5.4.8 Validation 186 5.5 Conclusions and Perspectives 189 References 189 6 System Suitability and Quality Control in GC-MS and GC×GC-MS 201 Anaïs Rodrigues, Djulia Bensaada, Jean-François Focant, and Pierre-Hugues Stefanuto 6.1 Introduction 201 6.1.1 Challenges in Nontargeted Analysis 202 6.
2 QA/QC Systems for Untargeted Metabolomics 202 6.2.1 Reference Materials for Untargeted Metabolomics 203 6.2.2 Lessons from Mass Spectrometry-Based Proteomics 204 6.3 System Suitability Testing in GC-MS 205 6.3.1 Definition and Purpose 205 6.
3.2 Instrument Maintenance and Troubleshooting 205 6.3.3 Key Parameters to Monitor in GC-MS 205 6.3.4 Standardized References for SST in GC-MS 206 6.3.4.
1 Synthetic Chemical Mixtures 206 6.3.5 Internal and External Standards 207 6.3.5.1 Biological and Matrix-based Reference Materials 208 6.3.5.
2 Pooled Quality Control Mixture 208 6.4 Advanced System Suitability for GC× GC-MS 209 6.4.1 Unique Considerations in GC× GC-MS 209 6.4.1.1 Modulation Efficiency 209 6.4.
2 Standardized Test Mixtures for GC×GC 213 6.4.2.1 Gasoline: Used to Monitor Separation Quality 213 6.4.2.2 Phillips Mix: Developed to Evaluate GC×GC Performance 213 6.4.
2.3 Century Mix: A 100-Compound Reference Mixture for Standardizing Column Sets 213 6.4.2.4 Prehistoric Adhesives Characterization: Used in GC× GC-TOFMS for Identifying Organic Residues in Archaeological Contexts 214 6.4.2.5 Forensic Decomposition Analysis: Applied to Monitor Volatile Organic Compounds in Tissue Decomposition 215 6.
4.3 In-house QC Mixture: Case of QC39 215 6.5 Quality Control Strategies for Nontargeted Screening in Omics 221 6.5.1 Statistical QC Tools 221 6.5.1.1 QC Charts 221 6.
5.1.2 Multivariate QC Charts - Introduction to Multivariate Tools 221 6.5.1.3 Sequence Design and QC Monitoring 222 6.5.2 A Concrete Example of Quality Control QC Strategy for HPLC-MS and GC-MS-Based Metabonomic Analysis 222 6.
6 Chemometric Tools for Quality Assurance in Annotation 224 6.6.1 Role of Retention Indices and Spectral Libraries in Compound Annotations 225 6.6.2 Spectral Libraries 225 6.6.3 Machine Learning Approaches for Better Annotation with Spectral Libraries 226 6.7 Future Trends and Innovations 226 6.
7.1 Automation in System Suitability Testing and Quality Control Workflows 227 6.7.2 Case I: AI and Machine Learning for Real-Time Monitoring 227 6.7.3 Case II: Advances in Hardware and Software 227 6.8 Conclusion 228 Acknowledgments 229 References 229 Section II Omics Applications 235 7 In-vivo and in-situ Analysis of Plant Volatilome: Strategies, Challenges, and Applications for Understanding Biogenic Volatile Organic Compound Emissions 237 Cecilia Cagliero and Carlo Bicchi List of Abbreviations 237 7.1 Introduction 238 7.
2 Sampling Strategies 239 7.2.1 Static-headspace (S-HS) 240 7.2.2 Dynamic Headspace (D-HS) 243 7.2.3 Direct Contact 246 7.3 Quantification with in-vivo and in-situ Analysis: A Complex Task 247 7.
4 Overview of Analytical Platforms 250 7.5 Applications 252 7.6 Conclusions and Future Trends 264 References 265 8.1 Part I - Specialized Metabolites in Biological Systems: Focus on Derivatized Metabolites in Human Studies 271 Jacopo Troisi and Martina Lombardi 8.1.1 Specialized Metabolites and Their Importance in Various Biological Processes 271 8.1.1.
1 Introduction 271 8.1.1.2 Role in Defense Mechanisms 272 8.1.1.3 Role in Signaling and Communication 273 8.1.
1.4 Role Adaptation to Environmental Stress 274 8.1.1.5 Significance in Pharmaceutical and Industrial Applications 275 8.1.1.6 Significance in Understanding Biological Interactions 278 8.
1.1.7 Disease Modeling and Drug Discovery 279 8.1.1.8 Environmental Toxicology 280 8.1.1.
9 Biomarker Discovery and Diagnostic Applications 281 8.1.1.9.1 Biomarker Discovery 281 8.1.1.9.
2 Diagnostic Application 282 8.1.1.9.3 Environmental and Exposure Biomarkers 282 8.1.2 Biosynthetic Pathways in Animals for Specialized Metabolite Production 283 8.1.
2.1 Shikimate-like Pathways 283 8.1.2.2 Terpenes 284 8.1.2.3 Polyketide/Fatty Acid Metabolism 285 8.
1.3 The Role of Derivatization in Enhancing Metabolite Analysis 286 8.1.3.1 Introduction 286 8.1.3.2 Techniques for Derivatization of Metabolites in GC Analysis 287 8.
1.3.2.1 Silylation 287 8.1.3.2.2 Acylation 291 8.
1.3.2.3 Methylation 291 8.1.3.2.4 Alkylation 292 8.
1.3.2.5 Esterification 293 8.1.3.3 Comparative Overview of Derivatization Strategies in GC-MS Metabolomics 296 8.1.
3.3.1 Considerations and Challenges 296 8.1.4 Future Perspectives and Challenges 301