FOODOMICS -- CONTENTS -- PREFACE -- CONTRIBUTORS -- 1 FOODOMICS: PRINCIPLES AND APPLICATIONS -- 1.1 INTRODUCTION TO FOODOMICS -- 1.1.1 Definition of Foodomics -- 1.1.2 Foodomics Tools -- 1.2 FOODOMICS APPLICATIONS: CHALLENGES, ADVANTAGES, AND DRAWBACKS -- 1.2.1 Food Safety, Quality, and Traceability -- 1.2.2 Transgenic Foods -- 1.2.3 Foodomics in Nutrition and Health Research -- 1.3 FOODOMICS, SYSTEMS BIOLOGY, AND FUTURE TRENDS -- ACKNOWLEDGMENTS -- REFERENCES -- 2 NEXT GENERATION INSTRUMENTS AND METHODS FOR PROTEOMICS -- 2.1 INTRODUCTION -- 2.1.1 History of Mass Spectrometry-Based Proteomics -- 2.1.2 Overview of Classical Proteomics Techniques -- 2.1.3 Sample Preparation Methods -- 2.2 EMERGING METHODS IN PROTEOMICS -- 2.2.1 Bottom-up and Top-down Proteomics -- 2.2.2 Methods for Quantitative Proteomics -- 2.2.3 Post-Translational Protein Modifications Identification Methods -- 2.3 THE MOVE FROM SHOTGUN TO TARGETED PROTEOMICS APPROACHES -- 2.3.1 Shotgun Proteomics -- 2.3.2 Targeted Proteomics -- 2.3.3 Tandem Mass Spectrometry versus Selected/Multiple Reaction Monitoring -- 2.3.4 Tandem Mass Spectrometry with Alternative Acquisition Methods -- 2.3.5 Applications of Targeted Approaches in Food Science -- 2.4 NEW INSTRUMENTAL METHODS FOR PROTEOMICS -- 2.4.1 Fragmentation Methods -- 2.4.2 High Mass Accuracy and Fast Scanning Instrumentation -- 2.4.3 New Hybrid Instruments -- 2.5 BIOINFORMATICS TOOLS -- 2.5.1 Algorithms for Protein Identification -- 2.5.2 Post-Translational Modifications Identification by Computational Methods -- 2.5.3 Processing and Analyzing Proteomics Data -- 2.5.4 Proteomics Data Repositories -- REFERENCES -- 3 PROTEOMIC-BASED TECHNIQUES FOR THE CHARACTERIZATION OF FOOD ALLERGENS -- 3.1 INTRODUCTION: WHAT IS FOOD ALLERGY? -- 3.2 FOOD ALLERGY: FEATURES AND BOUNDARIES OF THE DISEASE.

3.3 IMMUNOPATHOLOGY OF FOOD ALLERGY AND ROLE OF PROTEOMICS -- 3.4 IDENTIFICATION OF FOOD ALLERGY EPITOPES -- 3.4.1 The Epitopes of Food Allergy -- 3.4.2 Proteomic Strategies for Allergen Identification, Detection, and Quantification -- 3.4.3 Identification of Linear and Conformational Epitopes -- 3.5 EXPRESSION PROTEOMICS AND FUNCTIONAL PROTEOMICS IN FOOD ALLERGY -- 3.6 IDENTIFICATION OF ALLERGENS IN TRANSFORMED PRODUCTS -- 3.7 CONCLUDING REMARKS -- REFERENCES -- 4 EXAMINATION OF THE EFFICACY OF ANTIOXIDANT FOOD SUPPLEMENTS USING ADVANCED PROTEOMICS METHODS -- 4.1 INTRODUCTION -- 4.1.1 Oxidative Stress in Aging and Disease -- 4.1.2 Dietary Antioxidants -- 4.2 METHODS FOR STUDYING THE EFFICACY OF ANTIOXIDANTS -- 4.2.1 Carbonylation as a Universal Indicator of Oxidative Stress -- 4.2.2 Methods for Purifying Carbonylated Proteins from Complex Mixtures, Mechanistic Studies of Diseases, and the Impact of Antioxidants -- 4.3 STRATEGIES USED FOR PROTEOMIC ANALYSIS OF CARBONYLATED PROTEINS AND THE IMPACT OF ANTIOXIDANTS -- 4.3.1 Isolating Carbonylated Peptides -- 4.3.2 Targeting Carbonylated Proteins as a Group -- 4.3.3 Multidimensional Separation -- 4.4 STUDYING OXIDATION MECHANISMS -- 4.4.1 Direct Oxidation with ROS -- 4.4.2 Adducting of Advanced Lipid Peroxidation End Products to Proteins -- 4.4.3 Analysis of Advanced Glycation End Products -- 4.5 QUANTIFICATION OF CARBONYLATION SITES -- 4.5.1 Quantitation Using Stable Isotope Coding -- 4.5.2 Quantitation Using Targeted Proteomics Techniques -- 4.6 BIOMEDICAL CONSEQUENCE OF PROTEIN OXIDATION AND THE IMPACT OF ANTIOXIDANTS -- 4.7 REDOX PROTEOMICS AND TESTING THE EFFICACY OF ANTIOXIDANTS -- REFERENCES -- 5 PROTEOMICS IN FOOD SCIENCE -- 5.1 PROTEOMICS -- 5.1.1 Bottom-Up Proteomic Approach -- 5.1.2 Mass Spectrometry -- 5.1.3 Protein Identification -- 5.1.4 Quantitative Proteomics.

5.1.5 Posttranslational Modifications -- 5.1.6 Targeted Proteomics -- 5.1.7 Proteomics and Systems Biology -- 5.2 APPLICATIONS IN FOOD SCIENCE -- 5.3 SPECIES IDENTIFICATION AND GEOGRAPHIC ORIGIN -- 5.3.1 Food Labeling, Traceability, and Proteomics -- 5.3.2 Fish -- 5.3.3 Shellfish -- 5.3.4 Meat and Other Food Products -- 5.4 DETECTION AND IDENTIFICATION OF SPOILAGE AND PATHOGENIC MICROORGANISMS -- 5.4.1 Mass Spectrometry in Bacterial Identification -- 5.4.2 Food Microbial Proteomics -- 5.4.3 Spectrum Libraries -- 5.5 CHANGES DURING FOOD STORAGE AND PROCESSING AND THEIR RELATIONSHIP TO QUALITY -- 5.5.1 Postmortem Changes in Meat Proteins -- 5.5.2 Postmortem Changes in Fish Muscle Tissue -- 5.5.3 Preslaughter Conditions and Proteome Changes -- 5.5.4 Proteomics to Study Effects of Processing/Conservation Treatments -- 5.6 PROTEOMICS DATA INTEGRATION TO EXPLORE FOOD METABOLIC PATHWAYS AND PHYSIOLOGICAL ACTIVITY OF FOOD COMPONENTS -- 5.7 NUTRIPROTEOMICS -- 5.8 FINAL CONSIDERATIONS AND FUTURE TRENDS -- REFERENCES -- 6 PROTEOMICS IN NUTRITIONAL SYSTEMS BIOLOGY: DEFINING HEALTH -- 6.1 INTRODUCTION -- 6.2 FROM FOOD PROTEINS TO NUTRIPROTEOMICS -- 6.3 NUTRITIONAL PEPTIDE AND PROTEIN BIOACTIVES -- 6.3.1 Nutrition and Immunity-A Bioactive Perspective from Human Breast Milk -- 6.4 NUTRITIONAL PEPTIDE AND PROTEIN BIOMARKERS -- 6.4.1 Biomarkers in Nutrition -- 6.4.2 Nutrition and Immunity-A Biomarker Perspective -- 6.5 ECOSYSTEM-LEVEL UNDERSTANDING OF NUTRITIONAL HOST HEALTH -- 6.5.1 The Human Host and Their Gut Microbiota -- 6.6 CONCLUSIONS AND PERSPECTIVES -- REFERENCES -- 7 MS-BASED METHODOLOGIES FOR TRANSGENIC FOODS DEVELOPMENT AND CHARACTERIZATION -- 7.1 INTRODUCTION -- 7.2 CONTROVERSIAL SAFETY ASPECTS AND LEGISLATION ON GMOs -- 7.3 ANALYSIS OF GMOs: TARGETED PROCEDURES AND PROFILING METHODOLOGIES -- 7.3.1 Targeted Analysis -- 7.3.2 Profiling Methodologies.

7.4 CONCLUSIONS AND FUTURE OUTLOOK -- ACKNOWLEDGMENTS -- REFERENCES -- 8 MS-BASED METHODOLOGIES TO STUDY THE MICROBIAL METABOLOME -- 8.1 INTRODUCTION -- 8.2 THE GUT MICROBIOTA AND THEIR ROLE IN METABOLISM -- 8.3 METAGENOMICS -- 8.4 METABOLOMICS -- 8.5 MICROBIAL METABOLITES IN THE HUMAN GUT -- 8.6 ANALYSIS OF THE MICROBIAL METABOLOME -- 8.7 IMPLICATIONS FOR HUMAN HEALTH AND DISEASE -- 8.7.1 Implications for Obesity -- 8.7.2 Implications for Diabetes -- 8.7.3 Implications for Cardiovascular Disease -- 8.7.4 Implications for Inflammation and Cancer -- 8.8 SUMMARY -- ACKNOWLEDGMENTS -- REFERENCES -- 9 MS-BASED METABOLOMICS IN NUTRITION AND HEALTH RESEARCH -- 9.1 INTRODUCTION -- 9.2 MS-BASED METABOLOMICS WORKFLOW -- 9.3 METABOLOMICS IN NUTRITION-RELATED STUDIES -- 9.4 DIET/NUTRITION AND DISEASE: METABOLOMICS APPLICATIONS -- 9.5 OTHER APPLICATIONS IN NUTRITIONAL METABOLOMICS -- 9.6 INTEGRATION WITH OTHER "OMICS" -- 9.7 CONCLUDING REMARKS -- ACKNOWLEDGMENTS -- REFERENCES -- 10 SHAPING THE FUTURE OF PERSONALIZED NUTRITION WITH METABOLOMICS -- 10.1 INTRODUCTION -- 10.2 METABOLOMICS TECHNOLOGIES -- 10.2.1 Nuclear Magnetic Resonance -- 10.2.2 Gas Chromatography Hyphenated to Mass Spectrometry -- 10.2.3 Inductively Coupled Plasma Mass Spectrometry -- 10.2.4 Liquid Chromatography-Mass Spectrometry -- 10.2.5 Capillary-Electrophoresis Hyphenated to Mass Spectrometry -- 10.3 PERSONALIZED NUTRITION -- 10.3.1 Metabolomics-One of the Keys to Unlock the Potential of Personalized Nutrition? -- 10.3.2 Personalized Nutrition-From Population to the Individual -- 10.3.3 Challenges for Using Metabolomics for Personalized Nutrition -- 10.3.4 Challenges for Deciphering Nutritional Biomarkers -- 10.3.5 Reality versus Dreams in Personalized Nutrition-Examples with Biomarkers of Intake -- 10.3.6 Moving from Global-Population-Based Biomarkers to Individual Biomarkers.

10.3.7 Understanding Population and Individual Metabolic Needs and Predisposition Will Pave the Way Forward for Future Nutritional Applications -- 10.4 CONCLUSION -- REFERENCES -- 11 HOW DOES FOODOMICS IMPACT OPTIMAL NUTRITION? -- 11.1 INTRODUCTION -- 11.1.1 The Five Patterns of Nutrition -- 11.1.2 The Evolution of the "Optimal Nutrition" Concept -- 11.1.3 Nutrients as Signaling Molecules: Nutrition is Not Only Essential Nutrients -- 11.1.4 The Postgenomic Era -- 11.2 NUTRIGENOMICS -- 11.2.1 Nutrigenomics and Prevention of Chronic Diseases: Looking for Health-Related Nutritional Biomarkers -- 11.2.2 Advances in Nutrigenomics -- 11.2.3 Current Limitations of the Omics Techniques -- 11.2.4 Systems Biology -- 11.3 NUTRIGENETICS AND PERSONALIZED NUTRITION -- 11.3.1 Epigenetics -- 11.3.2 The Present of Nutrigenetics and Personalized Nutrition -- 11.4 THE ADDED VALUE OF FOODOMICS FOR THE FOOD INDUSTRY -- 11.4.1 Foodomics as a New Tool for Linking Nutrition Research and Industry -- 11.4.2 Using Foodomics to Achieve Scientific Evidence: A Critical Challenge for the Food Industry -- 11.4.3 Broader Approach to Optimal Nutrition: Application of Foodomics Technologies from Farm to Fork -- 11.4.4 Foodomics and Agriculture -- 11.4.5 Screening of Novel Bioactive Functional Foods -- 11.4.6 Livestock and Animal Production -- 11.4.7 Food Processing and Safety -- 11.4.8 Quality Assurance -- 11.4.9 Personalized Nutrition as a Future Challenge for the Food Industry -- 11.5 CONCLUDING REMARKS -- REFERENCES -- 12 LIPIDOMICS -- 12.1 DEFINITION AND ANALYTICAL CHALLENGES IN LIPIDOMICS -- 12.1.1 Lipids: Functions and Classification -- 12.1.2 The Lipidomics Pipeline -- 12.2 LIPIDOMICS IN NUTRITION AND HEALTH RESEARCH -- 12.2.1 Lipidomics and Human Nutritional Interventions -- 12.2.2 Lipidomics and Nutrition-Related Diseases -- 12.3 LIPIDOMICS AND FOOD SCIENCE.

12.3.1 Lipidomics and Food Quality.