Foodomics: Advanced Mass Spectrometry in Modern Food Science and Nutrition

Provides the latest "–omics" tools to advance the study of food and nutrition

The rapidly emerging field of foodomics examines food and nutrition by applying advanced "–omics" technologies in order to improve people′s health, well–being, and knowledge. Using tools from genomics, transcriptomics, epigenomics, proteomics, and metabolomics, foodomics offers researchers new analytical approaches to solve a myriad of current challenges in food and nutrition science.

This book presents the fundamentals of foodomics, exploring the use of advanced mass spectrometry techniques in food science and nutrition in the post–genomic era. The first chapter of the book offers an overview of foodomics principles and applications. Next, the book covers:

Modern instruments and methods of proteomics, including the study and characterization of food quality, antioxidant food supplements, and food allergens Advanced mass spectrometry–based methods to study transgenic foods and the microbial metabolome Mass spectrometry–based metabolomics in nutrition and health research Foodomics′ impact on our current understanding of micronutrients (phenolic compounds and folates), optimal nutrition, and personalized nutrition and diet related diseases Principles and practices of lipidomics and green foodomics Use of chemometrics in mass spectrometry and foodomics

The final chapter of Foodomics explores the potential of systems biology approaches in food and nutrition research. All the chapters conclude with references to the primary literature, enabling readers to explore individual topics in greater depth.

With contributions from a team of leading pioneers in foodomics, this book enables students and professionals in food science and nutrition to take advantage of the latest tools to advance their research and open up new areas of food and nutrition investigation.

Preface xiii

Contributors xv

1 Foodomics: Principles and Applications 1
Alejandro Cifuentes

1.1 Introduction to Foodomics 1

1.2 Foodomics Applications: Challenges, Advantages, andDrawbacks 6

1.3 Foodomics, Systems Biology, and Future Trends 11

Acknowledgments 12

References 12

2 Next Generation Instruments and Methods for Proteomics15
Marýa 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 Approaches34

2.4 New Instrumental Methods for Proteomics 40

2.5 Bioinformatics Tools 49

References 55

3 Proteomic–Based Techniques for the Characterization of FoodAllergens 69
Gianluca Picariello, Gianfranco Mamone, Francesco Addeo, ChiaraNitride, 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 Proteomics71

3.4 Identification of Food Allergy Epitopes 73

3.5 Expression Proteomics and Functional Proteomics in FoodAllergy 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 SupplementsUsing 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 CarbonylatedProteins 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 Impactof Antioxidants 112

4.7 Redox Proteomics and Testing the Efficacy of Antioxidants113

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 PathogenicMicroorganisms 140

5.5 Changes During Food Storage and Processing and TheirRelationship to Quality 144

5.6 Proteomics Data Integration to Explore Food MetabolicPathways 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 Health167
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 Health178

6.6 Conclusions and Perspectives 181

References 182

7 MS–Based Methodologies for Transgenic Foods Development andCharacterization 191
Alberto Valdes and Virginia Garcýa–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 Metabolome221
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 Research245
Clara Ibanez and Carolina Simó

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 Applications259

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 withMetabolomics 271
Max Scherer, Alastair Ross, Sofia Moco, Sebastiano Collino,François–Pierre Martin, Jean–Philippe Godin, PeterKastenmayer, 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, AnnaCrescenti, Francesc Puiggros, Manuel Suarez, and LluýsArola

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 Folates381
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 GenomicInstability Using a Combined Proteomic and Functional Approach387

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

13.6 Summary 397

Acknowledgments 399

References 399

14 Metabolomics Markers in Acute and Endurance/ResistancePhysical Activity: Effect of the Diet 405
Sonia Medina, Debora Villano, Jose Ignacio Gil, CristinaGarcýa–Viguera, Federico Ferreres, and AngelGil–Izquierdo

14.1 Introduction 405

14.2 Metabolomics Consequences of Physical Activity: Metabolitesand Physiological Pathways Affected 407

14.3 Metabolomics and Physical Activity: Effect of the Diet410

14.4 Concluding Remarks and Future Perspectives 411

Acknowledgments 412

References 412

15 MS–Based Omics Evaluation of Phenolic Compounds asFunctional Ingredients 415
Debora Villano, Sonia Medina, Jose Ignacio Gil, CristinaGarcýa–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 ofPolyphenol–Rich Foods 421

15.5 Human Metabolome in Low and Normal Polyphenol DietaryIntake 424

15.6 Concluding Remarks and Future Perspectives 424

Acknowledgments 425

References 425

16 Metabolomics of Diet–Related Diseases 429
Marcela A. Erazo, Antonia Garcýa, Francisco J. Ruperez, andCoral 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
Marýa Castro–Puyana, Jose A. Mendiola, Elena Ibanez, andMiguel 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 Traceability464

17.5 Conclusions and Future Outlook 467

Acknowledgments 468

References 468

18 Green Foodomics 471
Jose A. Mendiola, Marýa Castro–Puyana, Miguel Herrero, andElena 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 Ingredients476

18.4 Development of Green Analytical Processes for Foodomics482

18.5 Comparative LCA Study of Green Analytical Techniques: CaseStudy 493

18.6 Conclusion 497

Acknowledgments 498

References 498

19 Chemometrics, Mass Spectrometry, and Foodomics507
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 Research539
Matej Oresic

20.1 Systems Biology New Opportunity for Food andNutrition Research 539

20.2 Systems Approach to Identify Molecular Networks BehindHealth and Disease 542

20.3 Food Metabolome and its Effect on Host Physiology 544

20.4 Building A Systems Biology Platform for Food and NutritionResearch 545

20.5 Future Perspectives 546

References 547

Index 551

ALEJANDRO CIFUENTES, PhD, is Full Research Professor at the National Research Council (CSIC) in Madrid, Spain. He has authored more than 200 SCI papers and is Editor of two journals: TrAC Trends in Analytical Chemistry and Electrophoresis. Dr. Cifuentes was the first to define the new discipline of foodomics in an SCI journal. His research centers on the development of advanced analytical methods for foodomics, food quality and safety, as well as the isolation and identification of biologically active natural products.