Food Microbiology and Food Safety

Series Editor:Michael P. Doyle

Food Microbiology and Food Safety Series

The Food Microbiology and Food Safety series is published in conjunction with the International Association for Food Protection, a non-pro fi t association for food safety professionals. Dedicated to the life-long educational needs of its Members, IAFP provides an information network through its two scienti fi c journals (Food Protection Trends and Journal of Food Protection), its educational Annual Meeting, international meetings and symposia, and interaction between food safety professionals.

Series Editor

Michael P. Doyle, Regents Professor and Director of the Center for Food Safety, University of Georgia, Grif fi th, GA, USA

Editorial Board

Francis F. Busta, Director, National Center for Food Protection and Defense, University of Minnesota, Minneapolis, MN, USA Bruce R. Cords, Vice President, Environment, Food Safety & Public Health, Ecolab Inc., St. Paul, MN, USA Catherine W. Donnelly, Professor of Nutrition and Food Science, University of Vermont, Burlington, VT, USA Paul A. Hall, President, AIV Microbiology and Food Safety Consultants, LLC, Hawthorn Woods, IL, USA Ailsa D. Hocking, Chief Research Scientist, CSIRO—Food Science Australia, North Ryde, Australia Thomas J. Montville, Professor of Food Microbiology, Rutgers University, New Brunswick, NJ, USA R. Bruce Tompkin, Formerly Vice President-Product Safety, ConAgra Refrigerated Prepared Foods, Downers Grove, IL, USA

For further volumes: http://www.springer.com/series/7131

Fidel Toldrá � Leo M.L. Nollet Editors

Proteomics in Foods

Principles and Applications

Editors Fidel Toldrá Department of Food Science Instituto de Agroquimica y Tecnologia

de Alimentos (CSIC) Valencia, Spain

Leo M.L. Nollet Department of Applied Engineering Sciences University College Ghent Ghent , Belgium

ISBN 978-1-4614-5625-4 ISBN 978-1-4614-5626-1 (eBook) DOI 10.1007/978-1-4614-5626-1 Springer New York Heidelberg Dordrecht London

Library of Congress Control Number: 2012954090

© Springer Science+Business Media New York 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, speci fi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on micro fi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied speci fi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a speci fi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.

Printed on acid-free paper

Springer is part of Springer Science+Business Media (www.springer.com)

This book is dedicated to my father, Fidel Toldrá Graells, who suddenly passed away during the fi nal preparation of this book. He was an enthusiastic and great supporter of my research activity. I will always remember him.

–Fidel Toldrá

vii

Preface

Food proteomics constitute at this moment one of the most relevant and fast devel-oping areas in food science. This is a very dynamic fi eld, developing and changing very rapidly in recent years. This book provides readers with the recent advances and state of the art in food proteomics.

To achieve this goal, the book is divided into two approaches containing a total of 28 chapters. The fi rst part deals with the principles of proteomics, especially focused to understand the proteome, the extraction and fractionation techniques for proteins and peptides, followed by separation techniques such as 2-D electrophoresis and chromatography and the mass spectrometry applications and search in protein databases. The second part is focused on the applications in foods. This part deals with quality issues related to post-mortem processes in animal foods and quality traits for a wide variety of foods such as meat, fi sh, dairy, eggs, wine, beer, cereals, fruits, and vegetables, but also for the identi fi cation of bioactive peptides and pro-teins which are very important from a nutritional point of view. Furthermore, con-sumers are now extremely susceptible towards food safety issues and proteomics can help in assuring different safety aspects including food authenticity, detection of animal species in the food, markers of pathogen microorganisms, or identi fi cation of prions. All these issues are considered in this book.

This book is written by 72 distinguished international contributors from 15 coun-tries with solid experience and reputation, bringing together the existing knowledge with the current and future potential applications of proteomics in food science and technology. We wish to thank the production team at Springer and to express our gratitude to Susan Safren (Senior Editor) and Rita Beck (Assistant Editor) for their kind assistance in this book.

Valencia, Spain Fidel Toldrá, Ph.D. Ghent, Belgium Leo M.L. Nollet, Ph.D.

ix

Contents

Part I Principles of Proteomics

1 Understanding the Proteome ................................................................. 3Emøke Bendixen

2 Extraction/Fractionation Techniques for Proteins and Peptides and Protein Digestion ....................................................... 21Daniel Martínez-Maqueda, Blanca Hernández-Ledesma, Lourdes Amigo, Beatriz Miralles, and José Ángel Gómez-Ruiz

3 Primary Separation: 2-D Electrophoresis ............................................ 51Romina Pedreschi

4 Primary Separation: Chromatography ................................................ 69M.-Concepción Aristoy, Leticia Mora, Elizabeth Escudero, and Fidel Toldrá

5 Mass Spectrometry Applications ........................................................... 83Carla Soler, Josep Rubert, and Jordi Mañes

Part II Food Applications of Proteomics

6 Challenges and Applications of Proteomics for Analysis of Changes in Early Postmortem Meat ................................................. 103Honggang Huang and René Lametsch

7 Application of Proteomics for Analysis of Protein Modifications in Postmortem Meat ....................................................... 111Honggang Huang and René Lametsch

x Contents

8 Biological Markers for Meat Tenderness of the Three Main French Beef Breeds Using 2-DE and MS Approach ............................ 127Thibault Chaze, Jean-François Hocquette, Bruno Meunier, Gilles Renand, Catherine Jurie, Christophe Chambon, Laurent Journaux, Sylvie Rousset, Christophe Denoyelle, Jacques Lepetit, and Brigitte Picard

9 Dry-Cured Ham ...................................................................................... 147Leticia Mora and Fidel Toldrá

10 Evaluation of Fish Quality and Safety by Proteomics Techniques ...................................................................... 161Carmen Piñeiro and Iciar Martinez

11 Farmed and Wild Fish ............................................................................ 181Maria Filippa Addis

12 Fish Authentication ................................................................................. 205Mónica Carrera, Benito Cañas, and José M. Gallardo

13 Proteomics in Milk and Milk Processing .............................................. 223Qiang Zhang and Catherine J. Carpenter

14 Cheese Processing ................................................................................... 247Aldo Di Luccia, Michele Faccia, Caterina Incoronato, Filomena Inglese, Carmela Lamacchia, Sara Lamparelli, Mariaconsiglia Occidente, and Donato Matassino

15 Lactic Acid Bacteria in Fermented Foods ............................................ 261Françoise Rul, Monique Zagorec, and Marie-Christine Champomier-Vergès

16 Wine Quality ............................................................................................ 285Marzia Giribaldi

17 Eggs .......................................................................................................... 305Gustavo Martos, Elena Molina, and Iván López-Expósito

18 Fruits and Vegetables .............................................................................. 323Peter M. Bramley

19 Wheat Grain Proteomics for the Food Industry .................................. 341Angéla Juhász, Paula Moolhuijzen, Matthew Bellgard, Rudi Appels, and Frank Békés

20 Proteomics and Applications to Food Science in Rice ......................... 379Pingfang Yang, Mohammad-Zaman Nouri, and Setsuko Komatsu

21 Beer Proteomics....................................................................................... 399Gianluca Picariello, Chiara Nitride, Gianfranco Mamone, Takashi Iimure, Francesco Addeo, and Pasquale Ferranti

xiContents

22 Nutritionally Relevant Proteins ............................................................. 425Djuro Josić, Spomenka Kovac, and Dajana Gaso-Sokac

23 Relevance of Peptides Bioactivity in Foods ........................................... 447Keizo Arihara

24 The Role of Proteomics in the Discovery of Marker Proteins of Food Adulteration ............................................................................... 465Gianfranco Mamone, Gianluca Picariello, Chiara Nitride, Francesco Addeo, and Pasquale Ferranti

25 Evaluation of Genetically Engineered Crops Using Proteomics ..................................................................................... 503Agnès E. Ricroch and Marcel Kuntz

26 Microbial Proteomics for Food Safety .................................................. 515Jasminka Giacometti and Djuro Josić

27 Prion Biomarkers .................................................................................... 547Rhiannon L.C.H. Huzarewich, Philippe Simon, and Stephanie A. Booth

28 Proteomics of Filamentous Fungi .......................................................... 563Mark W.J. van Passel, Peter J. Schaap, and Leo H. de Graaff

Index ................................................................................................................. 579

xiii

Contributors

Francesco Addeo Istituto di Scienze dell’Alimentazione – Consiglio and Pasquale Ferranti Nazionale delle Ricerche (CNR) , Avellino , Italy

Dipartimento di Scienza degli Alimenti , Università di Napoli “Federico II” , Portici Napoli , Italy

Maria Filippa Addis Porto Conte Ricerche , Loc. Tramariglio , Alghero (SS) , Italy

Lourdes Amigo Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM, CEI UAM + CSIC) , Madrid , Spain

Rudi Appels Centre for Comparative Genomics , Murdoch University , Western Australia , Australia

Keizo Arihara Department of Animal Science , Kitasato University , Towada-shi , Japan

M.-Concepción Aristoy Instituto de Agroquímica y Tecnología de Alimentos (CSIC) , Paterna, Valencia , Spain

Emøke Bendixen Department of Molecular Biology and Genetics , Aarhus University , Aarhus , Denmark

Frank Békés FBFD PTY LTD , Beecroft , NSW , Australia

Matthew Bellgard Centre for Comparative Genomics , Murdoch University , Western Australia , Australia

Stephanie A. Booth Molecular Pathobiology, National Microbiology Laboratory , Public Health Agency of Canada , Winnipeg , MB , Canada

Department of Medical Microbiology , University of Manitoba , Winnipeg , MB , Canada

xiv Contributors

Peter M. Bramley School of Biological Sciences , Royal Holloway, University of London , Surrey , UK

Benito Cañas Complutense University of Madrid , Madrid , Spain

Catherine J. Carpenter Department of Chemistry and Biochemistry , University of California-Santa Barbara , Santa Barbara , CA , USA

Mónica Carrera Institute of Molecular Systems Biology (IMSB) , ETH Zürich , Zürich , Switzerland

Christophe Chambon Plateforme d’exploration du métabolisme, des gènes aux métabolites , INRA Centre de Clermont Ferrand , Theix , France

Marie-Christine Champomier-Vergès INRA, UMR1319 Micalis , Jouy-en-Josas , France

AgroParisTech, UMR Micalis , Jouy-en-Josas , France

Thibault Chaze INRA, UR1213 Herbivores , Saint-Genès-Champanelle , France

Christophe Denoyelle Institut de l’Elevage , Paris , France

Aldo Di Luccia Department of SAFE , University of Foggia , Foggia , Italy

ConSDABI , Benevento , Italy

Elizabeth Escudero Instituto de Agroquímica y Tecnología de Alimentos (CSIC) , Paterna (Valencia) , Spain

Leo H. de Graaff Systems and Synthetic Biology , Wageningen University , Wageningen , The Netherlands

Michele Faccia Department of DIBCA , University of Bari , Bari , Italy

Pasquale Ferranti Istituto di Scienze dell’Alimentazione – Consiglio and Pasquale Ferranti Nazionale delle Ricerche (CNR) , Avellino , Italy

Dipartimento di Scienza degli Alimenti , University of Naples “Federico II” , Portici , Napoli, Italy

José M. Gallardo Marine Research Institute , CSIC , Vigo, Pontevedra , Spain

Dajana Gaso-Sokac Food Technology, J.J. Strossmayer University of Osijek, Osijek, Croatia

Department of Chemistry , J.J. Strossmayer University of Osijek , Osijek , Croatia

Jasminka Giacometti Department of Biotechnology , University of Rijeka , Rijeka , Croatia

Marzia Giribaldi National Research Council – Institute of Sciences of Food Production , Grugliasco , TO , Italy

José Ángel Gómez-Ruiz Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM, CEI UAM + CSIC) , Madrid , Spain

xvContributors

Blanca Hernández-Ledesma Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM, CEI UAM + CSIC) , Madrid , Spain

Jean-François Hocquette INRA, UR1213 Herbivores , Saint-Genès-Champanelle , France

Honggang Huang Department of Food Science , University of Copenhagen , Frederiksberg , Denmark

Rhiannon L.C.H. Huzarewich Viral Diseases, National Microbiology Laboratory , Public Health Agency of Canada , Winnipeg , MB , Canada

Takashi Iimure Bioresources Research and Development Department , Sapporo Breweries Ltd , Ota , Gunma , Japan

Caterina Incoronato ConSDABI , Benevento , Italy

Filomena Inglese ConSDABI , Benevento , Italy

Djuro Josić Department of Biotechnology , University of Rijeka , Rijeka , Croatia

Warren Alpert Medical School , Brown University , Providence , RI , USA

Angéla Juhász Agricultural Institute , Centre for Agricultural Research of the Hungarian Academy of Sciences , Martonvásár , Hungary

Laurent Journaux UNCEIA, MNE , Paris , France

Catherine Jurie INRA, UR1213 Herbivores , Saint-Genès-Champanelle , France

Setsuko Komatsu National Institute of Crop Science , Tsukuba , Japan

Spomenka Kovac Food Technology, J.J. Strossmayer University of Osijek, Osijek, Croatia

Department of Chemistry , J.J. Strossmayer University of Osijek , Osijek , Croatia

Marcel Kuntz Laboratoire de Physiologie Cellulaire Végétale (UMR5168) , Université Joseph Fourier / CNRS / CEA / INRA , Grenoble , France

Carmela Lamacchia Department of SAFE , University of Foggia , Foggia , Italy

René Lametsch Department of Food Science , University of Copenhagen , Frederiksberg , Denmark

Sara Lamparelli Department of SAFE , University of Foggia , Foggia , Italy

Jacques Lepetit UR 370, Unité Qualité Produits Animaux, INRA , France

Iván López-Expósito Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM) , Madrid , Spain

Gianfranco Mamone Istituto di Scienze dell’Alimentazione (ISA) – CNR , Avellino , Italy

xvi Contributors

Jordi Mañes Departament de Medicina Preventiva i Salut Pública , Universitat de València , Burjassot , Spain

Iciar Martínez Department of Zoology and Cellular Biology , University of the Basque Country , Leioa , Spain

IKERBASQUE, Basque Foundation for Science , Bilbao , Spain

Daniel Martínez-Maqueda Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM, CEI UAM + CSIC) , Madrid , Spain

Gustavo Martos Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM) , Madrid , Spain

Donato Matassino ConSDABI , Benevento , Italy

Bruno Meunier INRA, UR1213 Herbivores , Saint-Genès-Champanelle , France

Beatriz Miralles Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM, CEI UAM + CSIC) , Madrid , Spain

Elena Molina Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM) , Madrid , Spain

Paula Moolhuijzen Centre for Comparative Genomics , Murdoch University , Western Australia , Australia

Leticia Mora Instituto de Agroquímica y Tecnología de Alimentos (CSIC) , Paterna, Valencia , Spain

Chiara Nitride Dipartimento di Scienza degli Alimenti, University of Naples “Federico II” , Portici I , Italy

Mohammad-Zaman Nouri Rice Research Institute of Iran-Deputy of Mazandaran , Amol , Iran

Mariaconsiglia Occidente ConSDABI , Benevento , Italy

Romina Pedreschi Food and Biobased Research , Wageningen , UR , The Netherlands

Brigitte Picard INRA, UR1213 Herbivores , Saint-Genès-Champanelle , France

Gianluca Picariello Istituto di Scienze dell’Alimentazione (ISA) – CNR , Avellino Italy

Carmen Piñeiro Institute for Marine Research (IIM) , Spanish Council for Scienti fi c Research (CSIC) , Vigo , Spain

Gilles Renand INRA, UMR1313 Génétique Animale et Biologie Intégrative , Jouy-en-Josas , France

xviiContributors

Agnès E. Ricroch Laboratoire Ecologie, Systématique et Evolution (UMR 8079) , Université Paris-Sud / CNRS / AgroParisTech , Orsay , France

Sylvie Rousset Centre de Recherche en Nutrition Humaine Auvergne, INRA , France

Josep Rubert Departament de Medicina Preventiva i Salut Pública , Universitat de València , Burjassot , Spain

Françoise Rul INRA, UMR1319 Micalis , Jouy-en-Josas , France

AgroParisTech, UMR Micalis , Jouy-en-Josas , France

Peter J. Schaap Systems and Synthetic Biology , Wageningen University , Wageningen , The Netherlands

Philippe Simon Special Pathogens, National Microbiology Laboratory , Public Health Agency of Canada , Winnipeg , MB , Canada

Department of Medical Microbiology , University of Manitoba , Winnipeg , MB , Canada

Carla Soler Departament de Medicina Preventiva i Salut Pública , Universitat de València , Burjassot , Spain

Fidel Toldrá Instituto de Agroquímica y Tecnología de Alimentos (CSIC) , Paterna, Valencia , Spain

Mark W. J. van Passel Systems and Synthetic Biology , Wageningen University , Wageningen , The Netherlands

Pingfang Yang Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture , Wuhan Botanical Garden, Chinese Academy of Science , Wuhan , China

Monique Zagorec INRA, UMR 1014 Secalim , 44307 Nantes , France

LUNAM Université, Oniris , Nantes, 44307 , France

Qiang Zhang Mead Johnson Nutrition Pediatric Nutrition Institute , Evansville , IN , USA