Contributors xv

1 Foodomics: Principles and Applications 1

Alejandro Cifuentes

1.1 Introduction to Foodomics 1

1.2 Foodomics Applications: Challenges, Advantages, and Drawbacks 6

1.3 Foodomics, Systems Biology, and Future Trends 11

Acknowledgments 12

References 12

2 Next Generation Instruments and Methods for Proteomics 15

Mar?a del Carmen Mena and Juan Pablo Albar

2.1 Introduction 15

2.2 Emerging Methods in Proteomics 19

2.3 The Move from Shotgun to Targeted Proteomics Approaches 34

2.4 New Instrumental Methods for Proteomics 40

2.5 Bioinformatics Tools 49

References 55

3 Proteomic-Based Techniques for the Characterization of Food Allergens 69

Gianluca Picariello, Gianfranco Mamone, Francesco Addeo, Chiara Nitride, and Pasquale Ferranti

3.1 Introduction: What is Food Allergy? 69

3.2 Food Allergy: Features and Boundaries of the Disease 70

3.3 Immunopathology of Food Allergy and Role of Proteomics 71

3.4 Identification of Food Allergy Epitopes 73

3.5 Expression Proteomics and Functional Proteomics in Food Allergy 81

3.6 Identification of Allergens in Transformed Products 85

3.7 Concluding Remarks 90

References 91

4 Examination of the Efficacy of Antioxidant Food Supplements Using Advanced Proteomics Methods 101

Ashraf G. Madian, Elsa M. Janle, and Fred E. Regnier

4.1 Introduction 101

4.2 Methods for Studying the Efficacy of Antioxidants 102

4.3 Strategies Used for Proteomic Analysis of Carbonylated Proteins and the Impact of Antioxidants 106

4.4 Studying Oxidation Mechanisms 107

4.5 Quantification of Carbonylation Sites 111

4.6 Biomedical Consequence of Protein Oxidation and the Impact of Antioxidants 112

4.7 Redox Proteomics and Testing the Efficacy of Antioxidants 113

References 117

5 Proteomics in Food Science 125

Jose M. Gallardo, Monica Carrera, and Ignacio Ortea

5.1 Proteomics 125

5.2 Applications in Food Science 132

5.3 Species Identification and Geographic Origin 132

5.4 Detection and Identification of Spoilage and Pathogenic Microorganisms 140

5.5 Changes During Food Storage and Processing and Their Relationship to Quality 144

5.6 Proteomics Data Integration to Explore Food Metabolic Pathways and Physiological Activity of Food Components 149

5.7 Nutriproteomics 150

5.8 Final Considerations and Future Trends 151

References 152

6 Proteomics in Nutritional Systems Biology: Defining Health 167

Martin Kussmann and Laurent Fay

6.1 Introduction 167

6.2 From Food Proteins to Nutriproteomics 171

6.3 Nutritional Peptide and Protein Bioactives 172

6.4 Nutritional Peptide and Protein Biomarkers 174

6.5 Ecosystem-Level Understanding of Nutritional Host Health 178

6.6 Conclusions and Perspectives 181

References 182

7 MS-Based Methodologies for Transgenic Foods Development and Characterization 191

Alberto Valdes and Virginia Garc?a-Canas

7.1 Introduction 191

7.2 Controversial Safety Aspects and Legislation on GMOs 192

7.3 Analysis of GMOs: Targeted Procedures and

Profiling Methodologies 193

7.4 Conclusions and Future Outlook 212

Acknowledgments 212

References 212

8 MS-Based Methodologies to Study the Microbial Metabolome 221

Wendy R. Russell and Sylvia H. Duncan

8.1 Introduction 221

8.2 The Gut Microbiota and Their Role in Metabolism 222

8.3 Metagenomics 224

8.4 Metabolomics 225

8.5 Microbial Metabolites in the Human Gut 226

8.6 Analysis of the Microbial Metabolome 229

8.7 Implications for Human Health and Disease 232

8.8 Summary 235

Acknowledgments 235

References 235

9 MS-Based Metabolomics in Nutrition and Health Research 245

Clara Ibanez and Carolina Simo

9.1 Introduction 245

9.2 MS-Based Metabolomics Workflow 246

9.3 Metabolomics in Nutrition-Related Studies 253

9.4 Diet/Nutrition and Disease: Metabolomics Applications 259

9.5 Other Applications in Nutritional Metabolomics 261

9.6 Integration with Other “Omics” 262

9.7 Concluding Remarks 263

Acknowledgments 264

References 264

10 Shaping the Future of Personalized Nutrition with Metabolomics 271

Max Scherer, Alastair Ross, Sofia Moco, Sebastiano Collino, Francois-Pierre Martin, Jean-Philippe Godin, Peter Kastenmayer, and Serge Rezzi

10.1 Introduction 271

10.2 Metabolomics Technologies 272

10.3 Personalized Nutrition 278

10.4 Conclusion 291

References 292

11 How Does Foodomics Impact Optimal Nutrition? 303

Anna Arola-Arnal, Josep M. del Bas, Antoni Caimari, Anna Crescenti, Francesc Puiggros, Manuel Suarez, and Llu?s Arola

11.1 Introduction 303

11.2 Nutrigenomics 310

11.3 Nutrigenetics and Personalized Nutrition 323

11.4 The Added Value of Foodomics for the Food Industry 329

11.5 Concluding Remarks 337

References 337

12 Lipidomics 351

Isabel Bondia-Pons and Tuulia Hyotylainen

12.1 Definition and Analytical Challenges in Lipidomics 351

12.2 Lipidomics in Nutrition and Health Research 360

12.3 Lipidomics and Food Science 368

12.4 Future Perspectives 371

References 372

13 Foodomics Study of Micronutrients: The Case of Folates 381

Susan J. Duthie

13.1 Folates in the Diet 381

13.2 Folate and Human Health 383

13.3 Measuring Folates in Human Biomonitoring 385

13.4 Folate and Colon Cancer: Establishing Mechanisms of Genomic Instability Using a Combined Proteomic and Functional Approach 387

13.5 Folate Deficiency and Abnormal DNA Methylation: A Common Mechanism Linking Cancer and Atherosclerosis 394

13.6 Summary 397

Acknowledgments 399

References 399

14 Metabolomics Markers in Acute and Endurance/Resistance Physical Activity: Effect of the Diet 405

Sonia Medina, Debora Villano, Jose Ignacio Gil, Cristina Garc?a-Viguera, Federico Ferreres, and Angel Gil-Izquierdo

14.1 Introduction 405

14.2 Metabolomics Consequences of Physical Activity: Metabolites and Physiological Pathways Affected 407

14.3 Metabolomics and Physical Activity: Effect of the Diet 410

14.4 Concluding Remarks and Future Perspectives 411

Acknowledgments 412

References 412

15 MS-Based Omics Evaluation of Phenolic Compounds as Functional Ingredients 415

Debora Villano, Sonia Medina, Jose Ignacio Gil, Cristina Garc?a-Viguera, Federico Ferreres, Francisco A. Tomas-Barberan, and Angel Gil-Izquierdo

15.1 Introduction 415

15.2 Use of Metabolomics in Nutritional Trials 416

15.3 Statistic Tools in Nutritional Metabolomics 421

15.4 Metabolomics from Clinical Trials after Intake of Polyphenol-Rich Foods 421

15.5 Human Metabolome in Low and Normal Polyphenol Dietary Intake 424

15.6 Concluding Remarks and Future Perspectives 424

Acknowledgments 425

References 425

16 Metabolomics of Diet-Related Diseases 429

Marcela A. Erazo, Antonia Garc?a, Francisco J. Ruperez, and Coral Barbas

16.1 Introduction 429

16.2 Analysis of the Metabolome: Metabolomics 431

16.3 Diet-Related Diseases 432

References 446

17 MS-Based Metabolomics Approaches for Food Safety, Quality, and Traceability 453

Mar?a Castro-Puyana, Jose A. Mendiola, Elena Ibanez, and Miguel Herrero

17.1 Introduction 453

17.2 MS-Based Metabolomics for Food Safety 455

17.3 MS-Based Metabolomics to Assess Food Quality 462

17.4 MS-Based Metabolomics Strategies for Food Traceability 464

17.5 Conclusions and Future Outlook 467

Acknowledgments 468

References 468

18 Green Foodomics 471

Jose A. Mendiola, Mar?a Castro-Puyana, Miguel Herrero, and Elena Ibanez

18.1 Basic Concepts of Foodomics (and How to Make it Greener) 471

18.2 Basic Concepts of Green Chemistry 472

18.3 Green Processes to Produce Functional Food Ingredients 476

18.4 Development of Green Analytical Processes for Foodomics 482

18.5 Comparative LCA Study of Green Analytical Techniques: Case Study 493

18.6 Conclusion 497

Acknowledgments 498

References 498

19 Chemometrics, Mass Spectrometry, and Foodomics 507

Thomas Skov and Søren B. Engelsen

19.1 Foodomics Studies 507

19.2 XC-MS Data 511

19.3 Data Structures and Models 517

19.4 Conclusion 534

References 535

20 Systems Biology in Food and Nutrition Research 539

Matej Oresic

20.1 Systems Biology—New Opportunity for Food and Nutrition Research 539

20.2 Systems Approach to Identify Molecular Networks Behind Health and Disease 542

20.3 Food Metabolome and its Effect on Host Physiology 544

20.4 Building A Systems Biology Platform for Food and Nutrition Research 545

20.5 Future Perspectives 546

References 547

Index 551

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