1、Methods inMolecular Biology 1072Jesus V. Jorrin-Novo Setsuko Komatsu Wolfram WeckwerthStefanie Wienkoop EditorsPlant ProteomicsMethods and ProtocolsSecond EditionME THODS IN MOLECULAR BIOLOGY Series EditorJohn M. Walker School of Life SciencesUniversity of Hertfordshire Hatfield, Hertfordshire, AL10

2、 9AB, UKFor further volumes:Plant ProteomicsMethods and Protocols Second EditionEdited byJesus V. Jorrin-NovoDepartment of Biochemistry and Molecular Biology, University of Cordoba, Cordoba, SpainSetsuko KomatsuNational Institute of Crop Science, National Agriculture and Food Research Organization,

3、Tsukuba, JapanWolfram Weckwerth and Stefanie WienkoopDepartment of Ecogenomics and Systems Biology, University of Vienna, Vienna, AustriaEditorsJesus V. Jorrin-Novo Department of Biochemistryand Molecular Biology University of Cordoba Cordoba, SpainWolfram Weckwerth Department of Ecogenomicsand Syst

4、ems Biology University of Vienna Vienna, AustriaSetsuko KomatsuNational Institute of Crop Science National Agriculture and Food ResearchOrganization Tsukuba, JapanStefanie Wienkoop Department of Ecogenomicsand Systems Biology University of Vienna Vienna, AustriaISSN 1064-3745ISSN 1940-6029 (electron

5、ic)ISBN 978-1-62703-630-6ISBN 978-1-62703-631-3 (eBook) DOI 10.1007/978-1-62703-631-3Springer New York Heidelberg Dordrecht LondonLibrary of Congress Control Number: 2013945305 Springer Science+Business Media, LLC 2014This work is subject to copyright. s are by the Publisher, whether the whole or pa

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7、ar 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 d specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of

8、 the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publishers 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 Copy

9、right 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 specific statement, that such names are exempt from the

10、 relevant protective laws and regulations and therefore 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

11、 that may be. The publisher makes no warranty, express or implied, with respect to the material contained herein.Printed on acid- paperHumana Press is a brand of SpringerSpringer is part of Springer Science+Business Media ()PrefaceThis book is the second one published on plant proteomics within this

12、 series. The first one, edited by H. Thiellement, M. Zivy, C. Damerval, and V. Mechin, appeared in 2007, 6 years ago, when 2-DE was almost the unique based platform for plant proteomics analysis. Since then, and iy short period of time, continuous improvements in techniques and pro- tocols for high-

13、throughput proteomics are being at all workflow stages, from wet (sampling, tissue and cell fractionation, protein extraction, depletion, purification, separa- tion, MS analysis, qufication) to dry lab (experimental design, algorithms for protein identification, bioinformatics tools for data analysi

14、s, databases, and repositories). In this book advances in the field of proteomics in the last 5 years and its application to plant biology and translational research are presented. It will help in exploiting the full potential of proteomics in plant biology research.It has been written by worldwide

15、recognized scientists, leaders in the field, and includes review pa workflows, methods, and techniques as well as ed protocols. It has been organized in nine parts, starting with a general one, in which the field is being reviewed from both a biological and methodological point of view. Part II is d

16、evoted to specific methodologies, with emphasis on second-, third-, and fourth-generation techniques (those of gel-, label- or label-, imaging, and targeted approaches). Applications of these techniques to the study of experimental m systems, crops, and orphan species (Part III), organs (Part IV), s

17、ubcellular fractions (Part V), and responses to stresses (Part VI) are included. Parts VII and VIII are devoted to the study and analysis of PTMs, protein inter- actions, and specific families of proteins. Part IX has been dedicated to the use of pro- teomics in translational research, with chapters

18、 on proteoty, beverage trazeability, and allergens. Finally, the last but not the least, Chapter 53 describes and discusses in standards required for a proteomics publication.Cordoba, SpainJesus V. Jorrin-NovoTsukuba, JapanSetsuko KomatsuVienna, AustriaWolfram WeckwerthVienna, AustriaStefanie Wienko

19、opvAcknowledgementTo my professors and referents Manuel Tena Aldave and Rafael Lopez Valbuena. They not only teached me, but, more important,me feel.viiContentsPreface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vAcknow

20、ledgementviiContributorsxvPART IINTRODUCTORY1 Plant Proteomics Methods and Protocols.3Jesus V. Jorrin-Novo2 From Proteomics to Systems Biology: MAPA, MASS WESTERN,PROMEX, and COVAIN as a User-Oriented Platform.15Wolfram Weckwerth, Stefanie Wienkoop, Wolfgang Hoehenwarter, Volker Egelhofer, and Xiaol

21、iang Sun3 Plant Proteomics: From Genome Sequencing to Proteome Databasesand Repositories29Katsumi Sakata and Setsuko Komatsu4 How to Use 2D Gel Electrophoresis in Plant Proteomics.43Thierry Rabilloud5 Standardization of Data Processing and Statistical Analysisin Comparative Plant Proteomics Experime

22、nt51Luis Valledor, M. Cristina Romero-Rodrguez, and Jesus V. Jorrin-Novo6 The Expanding Universe of Mass Analyzer Configurationsfor Biological Analysis61Juan J. CalvetePART IIEXPERIMENTAL7 A Protocol for Protein Extraction from Lipid-Rich Plant Tissues Suitablefor Electrophoresis.85Agnieszka Zienkie

23、wicz, Juan David Rejn, Juan de Dios Alch, Mara Isabel Rodrguez-Garca, and Antonio Jess Castro8 Making a Protein Extract from Plant PathogenicFungi for Gel- and LC-Based Proteomics.93Raquel Gonzlez Fernndez, Inmaculada Redondo, and Jesus V. Jorrin-Novo9 Plant Proteomics Methods to Reach Low-Abundance

24、 Proteins.111Egisto Boschetti and Pier Giorgio Righetti10 Combination of 2DE and LC for Plant Proteomics Analysis.131Sami Irar, Faial Brini, Khaled Masmoudi, and Montserrat Pagsix11 2DE Analysis of Forest Tree Proteins Using FluorescentLabels and Multiplexing141Jenny Renaut, Cline Leclercq, and Sbas

25、tien Planchon12 Differential Plant Proteome Analysis by Isobaric Tagsfor Relative and Absolute Qutation (iTRAQ)155Mara J. Martnez-Esteso, Juan Casado-Vela, Susana Sells-Marchart, Mara A. Pedreo, and Roque Bru-Martnez13 Global Qutative Proteomics Using Spectral Counting: An Inexpensive Experimental a

26、nd BioinformaticsWorkflow for Deep Proteome Coverage.171Tiago S. Balbuena, Diogo Ribeiro Demartini, and Jay J. Thelen14 Combining Chymotrypsin/Trypsin Digestion to IdentifyHydrophobic Proteins from Oil Bodies185Martimachova, Zita Purkrtova, Jiri Santrucek, Pascale Jolivet, Thierry Chardot, and Milan

27、 Kodicek15 Mass Western for Absolute Qufication of Target Proteinsand Considerations About the Instrument of Choice199David Lyon, Wolfram Weckwerth, and Stefanie Wienkoop16 Selected Reaction Monitoring Mass Spectrometry:A Methodology Overview209H. Alexander Ebhardt17 Mass Spectrometry-Based Imaging

28、of Metabolites and Proteins223Manuela Peukert, Michael Becker, Andrea Matros, and Hans-Peter Mock18 Using the Yeast Two-Hybrid System to IdentifyProteinProtein Interactions241Edgar Rodrguez-Negrete, Eduardo R. Bejarano, and Araceli G. Castillo19 Modifications of Wheat Germ Cell- Systemfor Functional

29、 Proteomics of Plant Membrane Proteins259Akira Nozawa and Yuzuru TozawaPART IIIBIOLOGICAL SYSTEMS20 Arabidopsis Proteomics: A Simple and Standardizable Workflowfor Qutative Proteome Characterization.275Anja Rdiger, Birgit Agne, Katja Baerenfaller, and Sacha Baginsky21 Analysis of Rice Proteins Using

30、 SDS-PAGE Shotgun Proteomics289Karlie A. Neilson, Iniga S. George, Samantha J. Emery, Sridevi Muralidharan, Mehdi Mirzaei, and Paul A. Haynes22 Medicago truncatula Proteomics for Systems Biology: Novel Rapid Shotgun LC-MS Approach for Relative Qufication Based on Full-Scan SelectivePeptide Extractio

31、n (Selpex)303M. Angeles Castillejo, Christiana Staudinger, Volker Egelhofer, and Stefanie Wienkoop23 Soybean Proteomics315Zahed Hossain and Setsuko KomatsuContentsxiii24 Proteome Analysis of Orphan Plant Species, Fact or Fiction?333Sebastien C. Carpentier and Twan America25 An Improved Detergent-Com

32、patible Gel-FractionationLC-LTQ-Orbitrap-MS Workflow for Plant and Microbial Proteomics347Luis Valledor and Wolfram WeckwerthPART IVDESCRIPTIVE PROTEOMICS26 Seed Proteomics361Jn A. Miernyk27 Back to Osborne. Sequential Protein Extraction and LC-MS Analysisfor the Characterization of the Holm Oak See

33、d Proteome379M. Cristina Romero-Rodrguez, Ana M. Maldonado-Alconada, Luis Valledor, and Jesus V. Jorrin-Novo28 Xylem Sap Proteomics391Thomas Dug de Bernonville, Ccile Albenne, Matthieu Arlat, Laurent Hoffmann, Emmanuelle Lauber, and Elisabeth Jamet29 Suspension-Cultured Plant Cells as a Tool to Anal

34、yzethe Extracellular Proteome.407Ana B. Sabater-Jara, Lorena Almagro, Sarai Belch-Navarro, Mara J. Martnez-Esteso, Sabry M. Youssef,Juan Casado-Vela, Juan C. Vera-Urbina, Susana Sells-Merchart, Roque Bru-Martnez, and Mara A. Pedreo30 Pollen Cultivation and Preparation for Proteomic Studies435Heidi P

35、ertl-Obermeyer and Gerhard ObermeyerPART VSUBCELLULAR PROTEOMICS31 Isolation of the Plant Cytosolic Fraction for Proteomic Analysis.453Gonzalo M. Estavillo, Yves Verhertbruggen, Henrik V. Scheller, Barry J. Pogson, Joshua L. Heazlewood, and Jun Ito32 Qutative Proteomic Analysis of Intact Plastids469

36、Takeshi Shiraya, Kentaro Kaneko, and Toshiaki Mitsui33 Shotgun Proteomics of Plant Plasma Membrane and Microdomain ProteinsUsing Nano-LC-MS/MS481Daisuke Takahashi, Bin Li, Takato Nakayama, Yukio Kawamura, and Matsuo Uemura34 Plant Mitochondrial Proteomics.499Shaobai Huang, Richard P. Jacoby, A. Harv

37、ey Millar, and Nicolas L. Taylor35 Separation of the Plant Golgi Apparatus and Endoplasmic Reticulumby-Flow Electrophoresis527Harriet T. Parsons, Susana M. Gonzlez Fernndez-Nio, and Joshua L. Heazlewood36 Isolation of Leaf Peroxisomes from Arabidopsisfor Organelle Proteome Analyses541Sigrun Reumann

38、and Rajneesh SinghalPART VICOMPARATIVE PROTEOMICS37 Proteomics of Field Samples in Radioactive Chernobyl Area.555Katarna Klubicov, Namik M. Rashydov, and Martin Hajduch38 Differential Proteome and Secretome Analysis DuringRicePathogen Interaction.563Yi Wang, Sang Gon Kim, Jingni Wu, Sun Tae Kim, and

39、 Kyu Young Kang39 Protein Extraction and Gel-Based Separation Methods to AnalyzeResponses to Pathogens in Carnation (Dianthus caryophyllus L).573Harold Duban Ardila, Raquel Gonzlez Fernndez, Blanca Ligia Higuera, Inmaculada Redondo, and Sixta Tulia MartnezPART VIIPOSTTRANSLATIONAL PROTEOMICS40 Stage

40、Tip-Based HAMMOC, an Efficient and Inexpensive Phosphopeptide Enrichment Method for Plant Shotgun Phosphoproteomics.595Hirofumi Nakagami41 Simultaneous Identification and Qufication of Nitrosylation Sitesby Combination of Biotin Switch and ICAT Labeling609Abasse Fares, Claude Nespoulous, Michel Ross

41、ignol, and Jean-Benot Peltier42 Tandem Metal-Oxide Affi Chromatography for Enhanced Depthof Phosphoproteome Analysis621Gerold J.M. Beckers, Wolfgang Hoehenwarter, Horst Rhrig, Uwe Conrath, and Wolfram Weckwerth43 N-Glycoprotein Enrichment by Lectin Affi Chromatography633Eliel Ruiz-May, Carmen Catal,

42、 and Jocelyn K.C. Rose44 Rapid and High-Throughput N-GlycomicAnalysis of Plant Glycoproteins.645Kentaro Kaneko, Takeshi Shiraya, Toshiaki Mitsui, and Shin-ichiro Nishimura45 Assay for Proteasome-Dependent Protein Degradationand Ubiquitinated Proteins655Takeo Sato, Kaori Sako, and Junji YamaguchiPART

43、 VIIIINTERACTOMICS AND PROTEINOMICS46 Separation of Membrane Protein Complexes by Native LDS-PAGE667Janine Arnold, Alexey Shapiguzov, Geoffrey Fucile, Jean-David Rochaix, Michel Goldschmidt-Clermont, and Lutz Andreas Eichacker47 Identification of Thioredoxin Target Disulfides Using Isotope-CodedAffi

44、 Tags677Per Hgglund, Jakob Bunkenborg, Kenji Maeda, Christine Finnie, and Birte Svensson48 Class III Peroxidases687Sabine Lthje, Claudia-Nicole Meisrimler, David Hopff, Tim Schtze, Jenny Kppe, and Katrin HeinoPART IXTRANSLATIONAL PROTEOMICS49 Proteoty of Holm Oak (Quercus ilex subsp. ballota) Proven

45、ancesThrough Proteomic Analysis of Acorn Flour709Jos Valero Galvn, Raquel Gonzlez Fernndez, Luis Valledor, Rafael Ma. Navarro Cerrillo, and Jesus V. Jorrin-Novo50 Immunoproteomics Analysis of Food Allergens725Rika Nakamura and Reiko Teshima51 Beer and Wort Proteomics737Takashi Iimure, Makoto Kihara,

46、 and Kazuhiro Sato52 Precipitation of Champagne Base Wine ProteinsPrior to 2D Electrophoresis.755Clara Cilindre53 The Minimal Information About a Proteomics Experiment (MIAPE)from the Proteomics Standards Initiative765Salvador Martnez-Bartolom, Pierre-Alain Binz, and Juan P. AlbarIndex781Contributor

47、sBIRGIT AGNE Institut fr Biochemie, Abteilung Pflanzenbiochemie, (Biozentrum), Martin-Luther-Universitt Halle-Wittenberg, Halle (Saale), GermanyJUAN P. ALBAR National Center for Biotechnology (CNB-CSIC), Madrid, SpainCCILE ALBENNE Ple de Biotechnologie Vgtale, LRSV, UMR 5546 Universit Paul SabatierT

48、oulouse 3/CNRS, Auzeville, Castanet-Tolosan, FranceJUAN DE DIOS ALCH Department of Biochemistry, Cell and Molecular Biology of Plants,Estacin Experimental del Zaidn, Consejo Superior de Investigaciones Cientficas (CSIC), Granada, SpainLORENA ALMAGRO Plant Peroxidases Group, Department of Plant Physi

49、ology, Faculty ofBiology, University of Murcia, Murcia, SpainTWAN AMERICA Plant Research International, Wageningen UR, Wageningen, The NetherlandsHAROLD DUBAN ARDILA Laboratory Research in Plant Metabolic Activities, Departmentof Chemistry, National University of Colombia, Bogot, ColombiaMATTHIEU AR

50、LAT LIPM, UMR CNRS-INRA 2594-441, Castanet-Tolosan, FranceJANINE ARNOLD Center for Organelle Research (CORE), University of Stavanger, Stavanger, NorwayKATJA BAERENFALLER Department of Biology, Plant Biotechnology, ETH Zurich,Zrich, SwitzerlandSACHA BAGINSKY Institut fr Biochemie, Abteilung Pflanzen

51、biochemie, Martin-Luther-Universitt Halle-Wittenberg, Halle (Saale), GermanyTIAGO S. BALBUENA Department of Plant Biology, Institute of Biology, University ofCampinas, Campinas, SP, BrazilMICHAEL BECKER Bruker Daltonik GmbH, Bremen, GermanyGEROLD J.M. BECKERS Department of Molecular Systems Biology,

52、 University of Vienna, Vienna, AustriaEDUARDO R. BEJARANO Departamento de Biologa Celular, Gentica y Fisiologa,Instituto de Hortofruticultura Subtropical y Mediterrnea “yora”, Universidad de MlagaConsejo Superior de Investigaciones Cientficas (IHSM-UMA-CSIC), Universidad de Mlaga, Mlaga, SpainSARAI

53、BELCH-NAVARRO Plant Peroxidases Group, Department of Plant Physiology,Faculty of Biology, University of Murcia, Murcia, SpainPIERRE-ALAIN BINZ Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva, SwitzerlandEGISTO BOSCHETTI EB-Consult, FranceFAIAL BRINI Plant Molecular Genetics Laboratory, C

54、entre of Biotechnology of Sfax (CBS), Sfax, TunisiaROQUE BRU-MARTNEZ Plant Proteomics and Functional Genomics Group,Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, SpainxvContributorsxxiJAKOB BUNKENBORG Center of Experimental BioInformatics, Depart

55、ment of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DenmarkJUAN J. CALVETE Instituto de Biomedicina de Valencia, CSIC, Valencia, SpainSEBASTIEN C. CARPENTIER Faculty of Bioscience Engineering, Department of Biosystems,K.U. Leuven, Leuven, Belgium; SYBIOMA: Facility fo

56、r Systems Biology Based Mass Spectrometry, Leuven, BelgiumJUAN CASADO-VELA Translational Oncology Unit, Instituto de Investigaciones BiomdicasAlberto Sols, Spanish National Research Council (CSIC-UAM), Madrid, SpainM. ANGELES CASTILLEJO Department of Molecular Systems Biology, University of Vienna, Vienna, AustriaARACELI G. CASTILLO Instituto de Hortofruticultura, Subtropicaly Mediterrnea,IHSM-UMA-C