Foodomics advanced mass spectrometry in modern food science and nutrition edited by alejandro cifuentes

FOODOMICS WILEY SERIES ON MASS SPECTROMETRY Series Editors Dominic M Desiderio Departments of Neurology and Biochemistry University of Tennessee Health Science Center Nico M M Nibbering Vrije Universiteit Amsterdam, The Netherlands A complete list of the titles in this series appears at the end of this volume FOODOMICS Advanced Mass Spectrometry in Modern Food Science and Nutrition Edited by ALEJANDRO CIFUENTES Laboratory of Foodomics (CIAL) National Research Council (CSIC) Madrid, Spain A JOHN WILEY & SONS, INC., PUBLICATION Copyright C 2013 by John Wiley & Sons, Inc All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permission Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose No warranty may be created or extended by sales representatives or written sales materials The advice and strategies contained herein may not be suitable for your situation You should consult with a professional where appropriate Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002 Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic formats For more information about Wiley products, visit our web site at www.wiley.com Library of Congress Cataloging-in-Publication Data Foodomics : advanced mass spectrometry in modern food science and nutrition / edited by Alejandro Cifuentes p cm Includes bibliographical references and index ISBN 978-1-118-16945-2 (cloth) Food–Analysis Mass spectrometry I Cifuentes, Alejandro, editor of compilation TX547.F66 2013 664 07–dc23 2012035736 Printed in the United States of America ISBN: 9781118169452 10 To the three women in my life, Susana, Claudia and Fernanda, every day they make of this world a better place to be A las tres mujeres de mi vida, Susana, Claudia y Fernanda, porque cada d´ıa ellas hacen de este mundo un lugar mejor donde vivir CONTENTS Preface Contributors Foodomics: Principles and Applications xiii xv Alejandro Cifuentes 1.1 Introduction to Foodomics 1.2 Foodomics Applications: Challenges, Advantages, and Drawbacks 1.3 Foodomics, Systems Biology, and Future Trends Acknowledgments References Next Generation Instruments and Methods for Proteomics 11 12 12 15 Mar´ıa del Carmen Mena and Juan Pablo Albar 2.1 Introduction 2.2 Emerging Methods in Proteomics 2.3 The Move from Shotgun to Targeted Proteomics Approaches 2.4 New Instrumental Methods for Proteomics 2.5 Bioinformatics Tools References 15 19 34 40 49 55 vii viii CONTENTS Proteomic-Based Techniques for the Characterization of Food Allergens 69 Gianluca Picariello, Gianfranco Mamone, Francesco Addeo, Chiara Nitride, and Pasquale Ferranti 3.1 3.2 3.3 3.4 3.5 Introduction: What is Food Allergy? Food Allergy: Features and Boundaries of the Disease Immunopathology of Food Allergy and Role of Proteomics Identification of Food Allergy Epitopes Expression Proteomics and Functional Proteomics in Food Allergy 3.6 Identification of Allergens in Transformed Products 3.7 Concluding Remarks References Examination of the Efficacy of Antioxidant Food Supplements Using Advanced Proteomics Methods 69 70 71 73 81 85 90 91 101 Ashraf G Madian, Elsa M Janle, and Fred E Regnier 4.1 Introduction 4.2 Methods for Studying the Efficacy of Antioxidants 4.3 Strategies Used for Proteomic Analysis of Carbonylated Proteins and the Impact of Antioxidants 4.4 Studying Oxidation Mechanisms 4.5 Quantification of Carbonylation Sites 4.6 Biomedical Consequence of Protein Oxidation and the Impact of Antioxidants 4.7 Redox Proteomics and Testing the Efficacy of Antioxidants References Proteomics in Food Science 101 102 106 107 111 112 113 117 125 Jos´e M Gallardo, M´onica Carrera, and Ignacio Ortea 5.1 5.2 5.3 5.4 Proteomics Applications in Food Science Species Identification and Geographic Origin Detection and Identification of Spoilage and Pathogenic Microorganisms 5.5 Changes During Food Storage and Processing and Their Relationship to Quality 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 125 132 132 140 144 149 150 151 152 CONTENTS Proteomics in Nutritional Systems Biology: Defining Health ix 167 Martin Kussmann and Laurent Fay 6.1 Introduction 6.2 From Food Proteins to Nutriproteomics 6.3 Nutritional Peptide and Protein Bioactives 6.4 Nutritional Peptide and Protein Biomarkers 6.5 Ecosystem-Level Understanding of Nutritional Host Health 6.6 Conclusions and Perspectives References 167 171 172 174 178 181 182 MS-Based Methodologies for Transgenic Foods Development and Characterization 191 Alberto Vald´es and Virginia Garc´ıa-Ca˜nas 7.1 Introduction 7.2 Controversial Safety Aspects and Legislation on GMOs 7.3 Analysis of GMOs: Targeted Procedures and Profiling Methodologies 7.4 Conclusions and Future Outlook Acknowledgments References 191 192 MS-Based Methodologies to Study the Microbial Metabolome 221 193 212 212 212 Wendy R Russell and Sylvia H Duncan 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 8.8 Summary Acknowledgments References MS-Based Metabolomics in Nutrition and Health Research 221 222 224 225 226 229 232 235 235 235 245 Clara Ib´an˜ ez and Carolina Sim´o 9.1 9.2 9.3 9.4 9.5 9.6 9.7 Introduction MS-Based Metabolomics Workflow Metabolomics in Nutrition-Related Studies Diet/Nutrition and Disease: Metabolomics Applications Other Applications in Nutritional Metabolomics Integration with Other “Omics” Concluding Remarks 245 246 253 259 261 262 263 x 10 CONTENTS Acknowledgments References 264 264 Shaping the Future of Personalized Nutrition with Metabolomics 271 Max Scherer, Alastair Ross, Sofia Moco, Sebastiano Collino, Franc¸ois-Pierre Martin, Jean-Philippe Godin, Peter Kastenmayer, and Serge Rezzi 11 10.1 Introduction 10.2 Metabolomics Technologies 10.3 Personalized Nutrition 10.4 Conclusion References 271 272 278 291 292 How Does Foodomics Impact Optimal Nutrition? 303 Anna Arola-Arnal, Josep M del Bas, Antoni Caimari, Anna Crescenti, Francesc Puiggr`os, Manuel Su´arez, and Llu´ıs Arola 12 11.1 Introduction 11.2 Nutrigenomics 11.3 Nutrigenetics and Personalized Nutrition 11.4 The Added Value of Foodomics for the Food Industry 11.5 Concluding Remarks References 303 310 323 329 337 337 Lipidomics 351 Isabel Bondia-Pons and Tuulia Hyăotylăainen 13 12.1 Denition and Analytical Challenges in Lipidomics 12.2 Lipidomics in Nutrition and Health Research 12.3 Lipidomics and Food Science 12.4 Future Perspectives References 351 360 368 371 372 Foodomics Study of Micronutrients: The Case of Folates 381 Susan J Duthie 13.1 13.2 13.3 13.4 Folates in the Diet Folate and Human Health Measuring Folates in Human Biomonitoring Folate and Colon Cancer: Establishing Mechanisms of Genomic Instability Using a Combined Proteomic and Functional Approach 13.5 Folate Deficiency and Abnormal DNA Methylation: A Common Mechanism Linking Cancer and Atherosclerosis 13.6 Summary Acknowledgments References 381 383 385 387 394 397 399 399 548 SYSTEMS BIOLOGY IN FOOD AND NUTRITION RESEARCH Gieger C, Geistlinger L, Altmaier E, Hrab´e de Angelis M, Kronenberg F, Meitinger T, Mewes HW, Wichmann HE, Weinberger KM, et al (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum PLoS Genetics 4(11):e1000282 Heinonen SM, Wahala K, Liukkonen KH, Aura AM, Poutanen K, Adlercreutz H (2004) Studies of the in vitro intestinal metabolism of isoflavones aid in the identification of their urinary 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metabolism in mice Journal of Lipid Research 51(5):1101–1112 550 SYSTEMS BIOLOGY IN FOOD AND NUTRITION RESEARCH Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al (2001) The sequence of the human genome Science 291(5507):1304– 1351 Virtue S, Vidal-Puig A (2010) Adipose tissue expandability, lipotoxicity and the metabolic syndrome—An allostatic perspective Biochimica Et Biophysica Acta 1801(3):338–349 von Bertalanffy L (1969) General Systems Theory New York: George Braziller Yu Z, Zhai G, Singmann P, He Y, Xu T, Prehn C, Răomisch-Margl W, Lattka E, Gieger C, Soranzo N, et al (2012) Human serum metabolic profiles are age dependent Aging Cell doi: 10.1111/j.1474-9726.2012.00865.x INDEX Acetoacetate, 408 Acute physical activity (APA), 405, 407, 409, 411 Acylcarnitines, 253, 408 Adenosine monophosphate, 408 Adenosylmethionine, Adiponectin, 441, 445 Alanine, 408 Alanine-glucose cycle, 407 Alignment, 509, 515, 516 Allantoine, 408 Allergenomics, 70 Allergoids, 91 Almond, see Diet intervention Amino acid, 246, 253, 254, 257–8, 260, 262 aromatic, 434 branched-chain amino acid (BCAA), 286, 434, 435, 438–9, 440 Ammonia, 227 Antibiotic, 455 Antibody, 171 Antimicrobial, 456 Antioxidant, 101, 257, 260, 473, 479, 493 Antiproliferative, 263 Apoptosis, 263 Apple, see Diet intervention AQUA peptides, 77–8 Ascorbic acid, 259, 263 Asparagine, 408 Atherosclerosis, 429, 430, 435, 439 risk factors, 439 Bacterial identification, 142–4 Banana, 411 Basophil activation test (BAT), 81, 84 Beta sitosterol, 259 Betaine, prolinebetaine, 255 Big-eights, 69 Bile acid, 228, 234–5, 259, 286, 439 Binning, 509, 511, 515 Bioactive, 167, 473, 476–82, 330–2, 334–5 Bioavailability, 261 Bioinformatics, 6, 11, 49–55, 167, 251–2 Biological variation, 257 Foodomics: Advanced Mass Spectrometry in Modern Food Science and Nutrition, First Edition Edited by Alejandro Cifuentes © 2013 John Wiley & Sons, Inc Published 2013 by John Wiley & Sons, Inc 551 552 INDEX Biomarker, 174, 246–249, 252–5, 259–260, 310–3, 331–2, 491–3 early, 311, 319 of nutrient exposure, 331 Body mass index (BMI), 287 Bottom-up, see Proteomics Bovine milk, see Milk Breast milk, see Milk Breast feeding, 172 Butyrate, 223 C reactive protein, 263 Caco-2 cell monolayers, 81 Caffeine, 418, 422 Cahill cycle, 407, 411 Caloric restriction, 257 Campesterol, 259 Cancer, 9–10, 233, 246, 259–61, 429, 430, 442, 491, 493 breast, 444 colon, 9–10, 261, 263 mouth, 442 prostate, 443 risk factors, 442 Capillary electrophoresis, see Electrophoresis Carbohydrates, 234 metabolism, 246, 257 Carbonylation, 102–117 Cardiovascular disease (CVD), 233, 263, 271, 286–7, 289, 429, 434 prognosis, 440 risk profile, 435 Carob, see Diet intervention Casein, 172 micelle, 173 Celiac disease, 86–9 Cell, 493 culture, 248, 253, 260 cycle, 263 disruption, 248 signaling, 168 Cerebrovascular disease (stroke), 430, 434, 436 risk factors, 437 Chemometrics, 454, 465 methods for data cubes, 531 methods for data tables, 519 Chocolate, see Diet intervention Choline, lysophosphatidylcholine, 259 Chromatin, Chromatography, 76, 78 2D, 76, 88 nanoHPLC chip, 78 nanoRP-HPLC, 88 Citrate, 408 Citric acid, 408 Citric acid cycle, 418, 422 Classification methods, 526 PLS-DA, 509, 526–9 other classifications methods, 529 Cocoa powder, see Diet intervention Colon model, 544 Combinatorial peptide ligand libraries (Proteominer), 90 Comparative safety assessment, 192, 198 Compounds bioactive, 9, 246, 253, 259–64 Consumer, 167, 329, 330, 337, 471, 479 Contaminants, 455 Coronary artery disease (CAD), 434 Coumaric acid, 259 Crohn’s disease, 260 Cross-reactive carbohydrate determinants (CCDs), 84 Cysteine, 408 Cystoseiraspp, 260 2-DGE, see Two-dimensional gel electrophoresis DART, see Direct Analysis in Real Time Data analysis, 512–3 Data cleaning, 509, 523 Data integration, 9, 11, 246, 249 Data quality (see Quality of data) Data structures, 517–8 Databases metabolomics, see Metabolomics Deficiency disease, 429 Delivery systems, Dental disease, 429 Depletion, 170 DESI, see Desorption electrospray ionization Desorption electrospray ionization, 464 Diabetes, 172, 232, 246, 259, 260, 271, 429, 430, 432 chronic complications, 433 insulin resistance, 286–7 INDEX prevalence, 433 risk factors, 433 type diabetes mellitus (T2DM), 279 Diagnostic marker, 168 Diarrhea, 172 Diet, 8, 167 intervention, 248, 252–64 mediterranean, 307 western, 306 Dietary, 329, 331–2, 335, 337 pattern, 329 treatment, 331, 332 Differential in gel electrophoresis (DIGE), 17, 22–4, 202 Differential stable isotope labeling, 23–26 DIGE, see Differential in gel electrophoresis Direct Analysis in Real Time, 464, 483–4 DNA, 4, 493 methylation, 4, 171 sequencing, Dynamic range, 169, 246 Dyslipidemia, 286 Ecosystem, 167, 496 Epigenetics, 171 EFSA, see European Food Safety Authority Electron ionization, 465 Electrophoresis, 173, 487, 491–3 CE-MS, 5, 195, 198, 204, 251, 260, 492, 494–5 differential gel (DIGE), 81 two-dimensional, 76, 81 Electrospray ionization (ESI), 17–9, 33, 41, 44, 46–7 Endurance/resistance physical activity (EPA), 407, 411 Energy metabolism, 256, 260 Environmental impact, 473, 475, 479, 481, 486, 497 Enzyme-linked immunosorbent assays (ELISA), 75, 83, 85, 88, 89 Epicatechin, 259 sulfate, 418, 420 O-methyl, 420 Epigenetic, 167 553 Epigenome, 168 Epitope, 73–74 conformational, 73–4 linear, 73–4 mapping, 79 ESI-IT, 128 European Food Safety Authority, Exercise intervention, 257–8 Expression Proteomics, 72, 81, 83 Faecalibacterium prausnitzii, 223, 225, 233, 235 Fat, see Diet intervention Fatty acids, 253, 255, 257–9, 263, 438–9 metabolism, 444 monounsaturated (MUFA), 441 omega-6/omega-3, 440 polyunsaturated (PUFA), 441 short chain, 223–4, 233 Fecapentanes, 234 FIA-MS/MS, 252 Fiber, 430 intake, 430, 440 Fingerprinting, 5, 454 metabolic, 247–8 Flow injection analysis, see FIA-MS/MS Folate, 381–403 absorption & metabolism, 383 blood status, 383, 385 LC MS/MS, 386–7, 388 microbiological assay, 385 protein binding assay, 385 chemical structure, 381–2 dietary sources, 381, 383 DNA methylation and gene expression, 394 cancer, colon, 395–7 CVD, 395–7 genomic stability, 387–93 global DNA methylation & LC MS/MS, 394–7 ApoE null mice, folate deficient, 397–8 rats, folate depleted, 397–8 human disease, 383–4, 397, 399 carbon metabolism, 383 cancer, colorectal (CRC), 384, 387, 393 cardiovascular disease (CVD), 384 554 INDEX Folate (Continued ) cognitive decline, 384 neural tube defects (NTDs), 384 protein expression & proteomic analyses, 388–94 colon cells, human, 388–91 colon, rat, 391–3 plasma, human, 393–4 Food adulteration, 132–4 allergens, 76–81 “hidden”, 75, 89 IgE-mediated, 72 non-IgE-mediated, 72 processing of, 86, 88 simulated gastrointestinal digestion of, 79–80 standardization of, 91 “type I” or complete, 72 “type II” or incomplete, 73 uptake of, 81 allergy, 69 prevalence, 71 immunopathology, 72–3 authentication, 132–5 conservation, 147–8 contaminants, 455 functional, 3, 329, 330–1, 335, 411, 471–3, 477–83 industry, 329–31, 336–7 labelling, 132–3 metabolic pathways, 149 metabolome, 453 new foods, origin, 465 physiological activity, 150 processing, 144, 147–8 product, 330 production, 331 proteome, 172 quality, 6, 144, 462–4 safety, 1, 6, 132, 139, 142, 147, 455–61 science, 167, 336 spoilage, 142 storage, 147–8 technology, 329 traceability, 1, 6, 132–4, 464–6 transgenic foods, 6–7, 191–212 Foodomics, 2, 125, 167, 329–37, 416–25 applications, basic concepts, 471 bioinformatics, colon cancer study, 10 definition, epigenomics, future trends, 11 GMO, 198, 212 Green, 471–98 metabolome, metabolomics, 5, 245, 261, 263 nutrition and health research, proteomics, scheme, tools, transcriptomics, Formate, 408 Fragmentation, 170 Fragmentation methods, 40 collision-activated dissociation (CAD), 41, 43 collision-induced dissociation (CID), 32, 40–1, 47–8 electron capture dissociation (ECD), 41 electron transfer dissociation (ETD), 41, 43, 46 high energy collisonal dissociation (HCD), 41, 46–7 Fruit ripening, Fumarate, 257, 408 Functional proteomics, 72, 83 Gallocatechin, 259 Gas Chromatography, 487 comprehensive two-dimensional GC, 458–9, 465 GC-FID, 208, 494–7 GC-MS, 5, 195, 205, 210, 251, 254–6, 260, 262, 456 large volume injection, 457 Gas-phase fractionation, 170 Gastrointestinal tract, 11, 167 GC, see Gas Chromatography Gene analysis, 493 expression, 253, 312, 318, 325–6 microarray, 199, 212 INDEX ontology, 173 regulation, 171 Generally Recognized As Safe, 477 Genetic predisposition, 167, 171 susceptibility, 171 Genetically modified organisms (GMO), 191 plant, 261 profiling methodologies, 193, 198 regulation, 192, 212 targeted analysis, 193–4, 198 Genome-Wide Association Studies (GWAS), 288–9 Germ-free mice, 262 Glucagon, 445 Gluconeogenesis, 430 Glucose-10-phosphate, 408 Glucose metabolism, 253, 257 Glutamate, 263 Glutamic acid, 408 Glutamine, 263, 408 Glycemia, 434 Glycerol, 259, 408 Glycine, 408 Glycogenolysis, 407–8 Glycolysis, 407, 409 Glycomic, 173 Glycosylation of proteins, 32–3, 43 GM crop, see Genetically modified organism barley, 195, 206 cucumber, 206 grapevine, 200, 206 maize, 191, 195, 200, 206 pea, 195, 200 potato, 191, 195, 200 raspberries, 206 rice, 191, 195, 200 soybean, 191, 195, 200 tomato, 195, 200 wheat, 191, 195, 200 GRAS, see Generally Recognized As Safe Grape juice, 254, 262 Green Analytical Chemistry, 474–6, 482–8, 490–3 Green tea (see Diet intervention), 411 Gut microbiota, 256, 260, 262 555 Hazelnut, see Diet intervention Health, 167, 310–11, 329–31, 335–6, 471, 473, 475, 482, 496, claims, 330 disease prevention, 310–12 trajectory, 167 Herbicide tolerance, 191, 195, 200 HILIC/LC, see Hydrophilic interaction liquid chromatography Hippurate, 408 Hippuric acid, 259 Histone, code, 171 Homeostasis, 4, 256, 311, 313, 318 Homovanillic acid, 419 Host metabolism, 167 HPLC, see Liquid Chromatography Hydroxybenzoic acid, 419 Hydroxyisobutyrate, 409 Hydroxyisovalerate, 409 Hydroxymethoxyphenyl-␥ -valerolactone sulfate, 418 Hydroxyphenylacetic acid, 418–9 Hydroxyphenylpropionic acid, 418–20 Hydroxyphenylvaleric acid, 418 Hydrophilic interaction liquid chromatography, 260, 488–9 Hypertension, 287, 440 Hypoxanthine, 408 Identification metabolites, see Metabolomics Immobilized metal affinity chromatography (IMAC), 32–3 Immune protection, 172 reponse, 168 Immunochemical detection, 194 Inductively coupled plasma, see Mass spectrometry, ICP-MS Inflammation, 233, 434 Inflammatory bowel disease, 172 Inosine, 408 Insects resistance, 191, 195, 200 Insulin, 252 resistance, 430, 437 Interindividual variability, 167 Intermap, 440 Intersalt, 440 Ion Mobility Spectrometry, 484 556 INDEX Ionization electron, 456 direct, 464 Ischemia heart disease, 430, 434–5 prognosis, 436 Isobaric tag for relative and absolute quantitation (iTRAQ), 22, 24–5, 27, 37, 53 Isoelectric focusing (IEF), 16, 21, 170 Isogenic, 257 Isotope-coded affinity tags (ICAT), 22–5, 37, 53 Isotope-coded protein label (ICPL), 22, 24–6, 37, 53 Isotopic pattern, 252 Isotopic ratio mass spectrometry, 465 iTRAQ, 196, 203 Kidney cancer, 260 Krebs cycle, 432 Lactate, 223, 233, 253, 263, 408 Lactation, 172 Lactoglobulin beta, 172 Lambert Beer’s law, 531–2 Large volume injection, 457 LCA, see Life Cycle Assessment LC-MS, see Liquid Chromatography Leptin, 445 Life Cycle Assessment, 473–4, 479, 481, 493–8 Lifestyle, 8, 262, 429, 431 Linoleic acid, 408 Lipidomics, 173, 277, 351, 483 analysis, 360 in food science, 368–74 in food quality, 369–70 in food safety, 370–1 Lipids, 351–4 analytical methods, 355–60 classification, 352–4 functions, 351–2 metabolism, 250, 253, 256, 257, 259 Lipogenesis, 430 Lipopolysaccharides (LPS), 233 Liquid Chromatography (LC), 169, 487–9, 494–6 LC-IRMS, 466 LC-MS, 5, 195–6, 199, 250–62, 457, 488, 491–6 LC-NMR, Ultra high Pressure Liquid Chromatography, 491 UPLC-MS, 204, 250–62, 455 Loadings, 520–1, 524 Luteolin, 445 Lysine, 260 Lysophosphatidylcholine, 259 Macronutrient, 167 Malate, 257, 408 Malate dehydrogenase, 263 MALDI, see Matrix Assisted Laser Desorption Ionization Mass accuracy, 169, 252 Mass spectrometer, 169, 485 Mass spectrometry, 103–6, 125, 127–8, 171, 226, 454 atmospheric pressure chemical ionization (APCI), 277 CE-MS, 5, 195, 198, 204, 251, 260, 492, 494–5 DART-MS, 464 DESI-MS, 464 desorption ionization on silicon (DIOS), 277 direct ionization, 464 electron impact ionization (EI), 273 electrospray ionization (ESI), 76 FT-ICR MS, 174, 206, 211, 250, 252, 254, 255, 261 GC-MS, 5, 195, 205, 210, 251, 254–6, 260, 262, 456 GCxGC-MS, 465 ICP-MS, 464, 465 Imaging, 486 ion trap analyzers, 84, 88, 277 IRMS, 465 LC-MS, 5, 195–6, 199, 204, 250–62, 457, 488, 491–6 Multiple Reaction Monitoring (MRM), 74, 77–78, 90, 456, 457, 460 MSn , 250 Orbitrap analyzer, 85, 86, 88, 89 Q-TOF hybrid analyzer, 82, 86 tandem, 76 triple quadrupole analyzer 78, 84 UPLC-MS, 455 INDEX Matrix Assisted Laser Desorption Ionization (MALDI), 17–9 128, 172, 195, 199, 203, 486 Matrix effects, 456 Metabolite, 272–4, 276–8, 284–8, 290–1, 320–2, 331–2 Metabolic, see also Metabolomics fingerprinting, 431, 435, 436 imprinting, 171 phenotype 434 profiling 431, 436 programming, 167 syndrome, 286–7, 291, 429, 437 Metabolism disorders, 432 lipid, 438 methylamine, 433 nucleotide, 432 Metabolome, 168, 245–264, 482, 492 food, 453 Metabolomics, 5, 225, 271–4, 453, 484–91, 543–5 databases, 252 data processing, 251, see also Statistical analysis definition, 453 fingerprinting, 5, 247–8, 454 human studies, 418 identification, 250–3 nutrimetabolomics, 279, 289 pattern, 252, 257–8 pharmacometabolomics, 279 plant metabolomics, 261 profiling, 5, 247, 254–6, 259–64, 453 target analysis, 5, 246–7, 417 untargeted, 424, 513 workflow, 509 Metagenome, 172 Metagenomics, 224–5 Metaproteome, 172 Metatranscriptomics, 225 Methionine, ␤-D-methyl glucopyranoside, 408 3-methyl-2-oxovalerate, 409 MIAPE (Minimum information about a proteomics experiment), 55 Microarray technology, 4, 310–5, 318, 321 gene microarrays, 199, 212 protein microarrays, 557 Microbe, 171 Microbiome, 11, 262, 434, 438 Microbiota, 11, 167, 172, 222, 260, 262 gut, 279–81, 284–91 Microfluidic, 492–3 Micronutrient, 167, 279, 283 Milk bovine, 173 breast, 172–3, 255, 262 formula-fed, 172–3 Minerals, 274, 281 MRM, 131 mRNA, 310, 313, 318, 322 MS, see Mass Spectrometry Multidimensional Protein Identification (MudPIT), 22, 34–5 Multiple reaction monitoring (MRM), 27, 34–5, 37–40, 456, 457, 460 Multiplexed proteomics (MP), 33 Multivariate approach, 510, 517 Myocardial infarction, 435 Nanoflow, 173 Naringenin-O-glucuronide, 418 Necrotizing enterocolitis, 172 Network biology, 542–3 Next-generation sequencing, 199 Niacinamide, 408 NMR, see Nuclear Magnetic Resonance Nonmodified counterparts, 191, 203 Non specific lipid transfer proteins (nsLTPs), 80 Normalization, 509, 515–7, 525 Northern blotting, 199 Nuclear Magnetic Resonance (NMR), 5, 198, 204, 212, 254–256, 483–4 imaging (MRI), 444 LC-NMR, Nut, see Diet intervention Nutraceuticals, 6, 260, 471–92 Nutrients, 429 signaling, 307 Nutriproteomics, 150–1 Nutrigenetics, 2, 245 Nutrigenomics, 3, 171, 245, 263, 310–2, 327, 329 Nutrimetabolomics, 310, 316, 320, 330, 331, 336 558 INDEX Nutriproteomics, 310, 315, 318 Nutrition, 329–31, 335–7, 361–8 evolution of, 304 history, 304–8 human interventions, 361–2 related- diseases, 362–8 cancer, 367–8 fatty liver disease, 366–7 hyperthension, 365 inflammatory disease, 365 obesity, 362–3 type diabetes mellitus, 364 optimal, 303–8, 329, 331, 335 patterns, 304, 306 personalized, 9, 245, 253, 271–2, 278–81, 336–7 profiles, 329 research, 329 Nutritranscriptomics, 310, 312–3, 313, 321 Nutritional intervention, 167, 252–64 proteomics, 167 Obesity, 172, 232, 246, 256, 286–9, 291, 429, 437 Oil, see also Diet intervention corn, 255, 257 fish, 254 olive, 255, 257 Oleic acid, 408 Omega 3, see Diet intervention Omics history, 308, 539–40 limitations, 321, 539–40 platforms, 11, 245–6, 262, 482 techniques, 320–2 Oral allergy syndrome, 72 Osteoporosis, 429, 430 Oxidative stress, 407–11, 434 2-oxoisocaproate, 409 2-oxoisovalerate, 409 2-oxoglutarate, 408 Palmitic acid, 408 Pantothenate, 257 PARAFAC, 509, 519, 531–4 PARAFAC2, 509, 519, 531–4 Pareto scaling, 521, 524 Partial Least Squares regression see Statistical analysis discriminant analysis (see PLS-DA), 510 Pathogen, 459 Pathway analysis metabolomics, 252–3 PCA, 509, 519, 520–6 things to be aware of when using PCA, 523 PCR, see Polymerase chain reaction Pectin, 224 Peak picking, 251 PeptideAtlas, 169 Peptide data processing, 169 labeling, 170 mass fingerprinting (PMF), 18, 49, 51 proteotypic, 77–8, 89–90 sequencing, 169 Periferical mononuclear blood cells (PBMC), 312–5, 318 Persistent organic pollutants, 458 Pesticide, 455 Phenylalanine, 408 Phenolic acids, 229 Phenotype, 174, 246–7 Phenylacetic acid, 229 Phenylacetylglutamine, 419 Phenylpropanoid, 228 3-Phosphoglycerate, 408 Phospholipid, 259 Phosphoproteomics, 32 Phytochemicals, 261 PHWE, see Pressurized Hot Water Extraction PLE, see Pressurized Liquid Extraction PLS-DA, 509, 526–8 Things to be aware of when using PLS-DA, 527 Validation, 527 Validation rules, 529 Polyamines, 227, 261 Polymerase chain reaction, 194 Real-time PCR, Polymorphisms, 9, 245 Polyphenol, 253–5, 259–63 rich beverages, 411 Polyunsaturated fatty Acid (PUFA), 271, 288 INDEX Post-genomic, 246 Postharvest, Post-mortem changes, 144–6 Post-traslational modifications (PTMs), 18–21, 26, 31–3, 131, 169 computational methods, 50, 52 instrumental methods, 41, 43–6 Precursor ion, 170 Pre-processing, 515 Alignment, 509, 515–6 Binning, 509, 511, 515 Filtering, 509, 515 Baseline subtraction, 509, 515 Normalization, 509, 515–7, 525 Validation, 525 Pressurized Hot Water Extraction, 477–82, 486 Pre-slaughter conditions, 146–7 Pressurized Liquid Extraction, 477–8, 486 PRIDE (PRoteomics IDEntifications), 51, 53–4 Principal components analysis, see Statistical analysis and PCA Profiling, 5, 453, 487, 490, 492 metabolic, 5, 247, 254–6, 259–64, 493 Prolamin superfamily, 80 Prolinebetaine, 255 Propionate, 233 Protected designation of origin, 465 Protected geographical indication, 465 Proteins annotation, 171 bioavailability, 171 bioefficacy, 171 coding gene, 171 deep sequencing, 172 fish, 135, 137–8, 146, 148 identification, 128–9, 169, 491, 493 information and knowledge extractor (PIKE), 53 isoform, 169 meat, 139–40, 144–6, 147, 148 metabolism, 227, 234 microarrays, milk, effect of processing and storage, 148 milk, identification of pathogens, 143 milk, interactome map, 149 shellfish, 138–9 559 Proteome, 310, 318–9 Proteomics, 4–5, 101, 103, 171, 260, 263, 472, 482–3, 487, 490–2 bottom-up, 5, 19–21, 34, 126–7, 199 gel-based, 126 label-free, 22, 27–8, 30–2, 37, 53 quantitative, 129 shotgun, 30, 34–5, 38, 76–7, 127, 174, 203 targeted, 34–40 top-down, 5, 19–21, 41, 46, 126 Pyrogallol, 419–20 Pyruvate, 408 Quadrupole, 19, 36–41, 43–48 Qualitative data, 516–7 Quality control samples (QC samples), 514, 523 Quality control sample set, 250 Quality of the data, 514–5 Quantitative data, 517 QuEChERS, 458 Quenching, 247 Quinic acid, 259 Real-time PCR, see Polymerase chain reaction Red wine, 254, 255, 262 Regulation homeostatic, 4, 256 Regulatory system, 330 Repositories, proteomics data, 36, 53–4 Resveratrol, see Diet intervention RNA non-coding, RNA-Seq, see Next-generation sequencing Rosemary extract, 260–1, 473, 477, 479–82, 493, 496 Sample preparation, 5, 247, 249–50, 472, 482, 484, 492, 494, 496–7 Green, 476, 483, 485–7 Scores, 520–2 Selected reaction monitoring (SRM), 31–2, 34, 36–9 Serotonin, 253, 420, 424, 438 SFE, see Supercritical Fluid, Extraction Shotgun, see Proteomics Single nucleotide polymorphism (SNP), 7, 280, 288 Sitosterol beta, see Beta sitosterol 560 INDEX SMIM, 131 SNPs, see Single nucleotide polymorphism Solid phase extraction, 458 Spectral counting, 28–31 Spectrum libraries, 144 SRM, 131 Stable isotope labeling by amino acids in cell culture (SILAC), 22, 24, 26, 37, 53 Stable isotope labeling of mammals (SILAM), 22, 24 Stable isotope standards and capture by anti-peptide antibodies (SISCAPA), 27, 39 Starch, resistant, 224 Statistical analysis HCA, 173, 252, 253 PCA, 252, 454 PLS-DA, 252, 253, 257–258, 454 Structural elucidation, 252 Substantial equivalence, 192, 209 Succinate, 257, 408 Sulfate reducing bacteria, 234 Supercritical Fluid chromatography, 487–8 extraction, 477–82, 486, 494, 496 Surface-enhanced laser desorption ionization (SELDI), 18, 35 Systems biology, 11, 132, 262–3, 283, 289, 320, 322, 541–7 platform 545–6 Systems level, 167 Systems Response Profiles (SRPs), 283 Tandem mass spectrometry (MS/MS), 19–21, 33–5, 39–41, bioinformatics tools 50–1, 54 new instrumental methods, 43–9 quantification, 24, 26–31 Tandem mass tag (TMT), 23–5, 27 Targeted proteomics, 131–2 Taurine, 259, 408 Terpenoids, 228 Thrifty genotype, 430 Tocopherol, 259, 263 Tomato, see Diet intervention Top-down, see Proteomics Toxin, 459 Tract intestinal, seeGastrointestinal tract Training sample set, 250 Transcriptome, 168 Transgenic foods, 191 Treatment heating, 147–8 high-pressure, 148 Triacylglycerol, 259 Tricarboxylic acid cycle (TCA), 257, 407, 411 Trimethylamine N-oxide, 409 Tryptophan, 408 Two-dimensional gas chromatography, see Gas chromatography Two-dimensional gel electrophoresis (2-DGE), 15–7, 22–3, 199, 212, Unintended effects, 192–3, 198, 204 UPLC, see Liquid Chromatography, Ultra High Pressure Urea cycle, 435 Urolithin, 420–4 Validation, 525, 527–9 Validation sample set, 250 Valine, 408 Vanillic acid, 419–20 Variable selection, 530 Vitamins, 228, 281, 283 Vitamin B6, Vitamin B12, Vitamin C, 259, 263 Vitamin D, 280 Vitamin E, see Tocopherol Well-being, 167 Whey, 172 Wine (see Red wine), 419, 422–3 Workflow, 354–5 Xanthine, 408 XC-MS data, 509, 511–2 WILEY SERIES ON MASS SPECTROMETRY Series Editors Dominic M Desiderio Departments of Neurology and Biochemistry University of Tennessee Health Science Center Nico M M Nibbering Vrije Universiteit Amsterdam, The Netherlands John R de Laeter r Applications of Inorganic Mass Spectrometry Michael Kinter and Nicholas E Sherman r Protein Sequencing and Identification Using Tandem Mass Spectrometry Chhabil Dass r Principles and Practice of Biological Mass Spectrometry Mike S Lee r LC/MS Applications in Drug Development Jerzy Silberring and Rolf Eckman r Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research J Wayne Rabalais r Principles and Applications of Ion Scattering Spectrometry: Surface Chemical and Structural Analysis Mahmoud Hamdan and Pier Giorgio Righetti r Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology Igor A Kaltashov and Stephen J Eyles r Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition Isabella Dalle-Donne, Andrea Scaloni, and D Allan Butterfield r Redox Proteomics: From Protein Modifications to Cellular Dysfunction and Diseases Silas G Villas-Boas, Ute Roessner, Michael A.E Hansen, Jorn Smedsgaard, and Jens Nielsen r Metabolome Analysis: An Introduction Mahmoud H Hamdan r Cancer Biomarkers: Analytical Techniques for Discovery Chabbil Dass r Fundamentals of Contemporary Mass Spectrometry Kevin M Downard (Editor) r Mass Spectrometry of Protein Interactions Nobuhiro Takahashi and Toshiaki Isobe r Proteomic Biology Using LC-MS: Large Scale Analysis of Cellular Dynamics and Function Agnieszka Kraj and Jerzy Silberring (Editors) r Proteomics: Introduction to Methods and Applications Ganesh Kumar Agrawal and Randeep Rakwal (Editors) r Plant Proteomics: Technologies, Strategies, and Applications Rolf Ekman, Jerzy Silberring, Ann M Westman-Brinkmalm, and Agnieszka Kraj (Editors) r Mass Spectrometry: Instrumentation, Interpretation, and Applications Christoph A Schalley and Andreas Springer r Mass Spectrometry and Gas-Phase Chemistry of Non-Covalent Complexes Riccardo Flamini and Pietro Traldi r Mass Spectrometry in Grape and Wine Chemistry Mario Thevis r Mass Spectrometry in Sports Drug Testing: Characterization of Prohibited Substances and Doping Control Analytical Assays Sara Castiglioni, Ettore Zuccato, and Roberto Fanelli r Illicit Drugs in the Environment: Occurrence, Analysis, and Fate Using Mass Spectrometry ´ Angel Garci´a and Yotis A Senis (Editors) r Platelet Proteomics: Principles, Analysis, and Applications Foodomics: Advanced Mass Spectrometry in Modern Food Science and Nutrition, First Edition Edited by Alejandro Cifuentes © 2013 John Wiley & Sons, Inc Published 2013 by John Wiley & Sons, Inc Luigi Mondello r Comprehensive Chromatography in Combination with Mass Spectrometry Jian Wang, James MacNeil, and Jack F Kay r Chemical Analysis of Antibiotic Residues in Food Walter A Korfmacher (Editor) r Mass Spectrometry for Drug Discovery and Drug Development Alejandro Cifuentes (Editor) r Foodomics: Advanced Mass Spectrometry in Modern Food Science and Nutrition ... Netherlands A complete list of the titles in this series appears at the end of this volume FOODOMICS Advanced Mass Spectrometry in Modern Food Science and Nutrition Edited by ALEJANDRO CIFUENTES. .. Foodomics : advanced mass spectrometry in modern food science and nutrition / edited by Alejandro Cifuentes p cm Includes bibliographical references and index ISBN 978-1-118-16945-2 (cloth) Food? ??Analysis... proteins about the same time (O’Farrell, 1975) In 1994 the term “proteome” was coined (Wilkins Foodomics: Advanced Mass Spectrometry in Modern Food Science and Nutrition, First Edition Edited by Alejandro