Technologies

2 GEL-BASED PROTEOMICS 11

Pier Giorgio Righetti, Paolo Antonioli, Carolina Simo, and Attilio Citterio

2.1 Introduction and Brief Bibliographic Review 11

2.2 SDS-PAGE 12

2.3 IEF 17

2.4 2D Maps 22

2.5 Conclusions 28

2.6 Five-Year Viewpoint 29 References 30

3 MASS SPECTROMETRY-BASED PROTEOMICS: IDENTIFYING

PLANT PROTEINS 33

Eveline Bergm├╝ller, Sacha Baginsky, and Wilhelm Gruissem

3.1 Introduction and Brief Bibliographic Review 33

3.2 Instrumentation 34

3.3 MALDI 35

3.4 ESI 36

3.5 Mass Analyzers 36

3.6 Ion Detectors 38

3.7 Sample Preparation 39

3.8 Protein Identification 40

3.9 Conclusions 44

3.10 Five-Year Viewpoint 44 References 44

4 CHEMICAL PROTEOMICS 47

Miriam C. Hagenstein, Olaf Kruse, and Norbert Sewald

4.1 Introduction 47

4.2 Strategies For Activity-Based Protein Profiling (ABPP) 47

4.3 Case Study: Development of Molecular Tools Targeting Plant

Kinases 53

4.4 Conclusions 57

4.5 Five-Year Viewpoint 58 References 58

5 THE ARABIDOPSIS LOCALIZOME: SUBCELLULAR PROTEIN LOCALIZATION AND INTERACTIONS IN ARABIDOPSIS 61

Georgios Kitsios, Nicolas Tsesmetzis, Max Bush, and John H. Doonan

5.1 Protein Compartmentalization in Plant Cells 61

5.2 Experimental Determination of Protein Localization 66

5.3 In Vivo Imaging Approaches to Protein Localization and Interaction 69

5.4 Plant Cell Cultures for Studying Protein Localization 73

5.5 Protein-Protein Interaction In Vivo: FRET 74

5.6 Perspectives: Integrating Predictive and Experimental Protein Localization Data 77

References 77

6 SECRETOME: TOWARD DECIPHERING THE SECRETORY PATHWAYS AND BEYOND 83

Young-Ho Jung, Ganesh Kumar Agrawal, Randeep Rakwal, and Nam-Soo Jwa

6.1 Introduction and Brief Bibliographic Review 83

6.2 Methodology and Strategy 86

6.3 A Case Study: In Planta and In Vitro Protein Profiles of Soluble and Secreted Proteins in Rice 87

6.4 Conclusions 87

6.5 Five-Year Viewpoint 89 References 89

7 PEPTIDOMICS 91

Peter Schulz-Knappe

7.1 Introduction and Brief Bibliographic Review 91

7.2 Separation Technology 93

7.3 MS Technology 95

7.4 Bioinformatics and Data Mining 97

7.5 Differential Peptide Display 98

7.6 ID LC-MALDI 99

7.8 Applications 100

7.9 Peptides and Proteases 101

7.10 Conclusions 102

7.11 Five-Year Viewpoint 103 References 103

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