目录 前言 v 撰稿人 ix 第一部分 引言 1. 蛋白质组学简介 3 Friedrich Lottspeich 第二部分 电泳分离 2. 高分辨率二维电泳 13 Walter Weiss and Angelika Gorg 3. 非经典二维电泳 33 JacquelineBurre，Ilka Wittig，and Hermann Schagger 4. 蛋白质检测与定量技术用于基于凝胶的蛋白质组学分析 59 Walter Weiss，Florian Weiland，and Angelika Gorg 第三部分 质谱和串联质谱的应用 5. 基质辅助激光解吸电离质谱 85 Rainer Cramer 6. 毛细管电泳质谱联用应用于人尿液蛋白质组学分析与生物标志物发现 105 PetraZurbig，Eric Schiffer，and Harald Mischak 7. 多肽纳升级液相色谱指南 123 Thomas Frohlich and Georg J.Arnold 8. 多维蛋白鉴定技术 143 Katharina Lohrig and Dirk Wolters 9. 肽段为中心的蛋白质组学技术分析血小板蛋白 155 Oliver Simon，Stefanie Wortelkamp，and Albert Sickmann 10. 高分辨率质谱蛋白质组分析技术鉴定小鼠小肠20S蛋白质组分子组成 173 Reinhold Weber，Regina Preywisch，Nikolay Youhnovski，Marcus Groettrup，and Michael Przybylski 第四部分 蛋白质组学定量技术 11. 基于液相色谱质谱联用的定量蛋白质组学 189 Michael W.Linscheid，Robert Ahrends，Stefan Pieper，and Andreas Kuhn 12. 胶内酶切同位素标记蛋白质技术用于相对定量 207 Carla Schmidt and Henning Urlaub 13.电喷雾质谱技术用于血浆蛋白质组定量分析 227 Hong Wang and Sam Hanash 第五部分 质谱数据解读 14. 算法和数据库 245 Lennart Martens and Rolf Apweiler 15. 鸟枪法蛋白质鉴定和质谱法蛋白质定量 261 Bingwen Lu，Tao Xu，Sung Kyu Park，and John R.Yates III 第六部分 蛋白质修饰分析 16. 脑蛋白氧化修饰蛋白质组学鉴定 291 Rukhsana Sultana，Marz ia Perluigi，and D.Allan Butter field 17.同位素标记、磷酸化多肽亲和富集技术用于液相色谱-串联质谱蛋白质组分析 303 Uma Kota，Ko-yi Chien，and Michael B.Goshe 第七部分 亚细胞蛋白质组学 18. 细胞器蛋白质组学：天然蛋白胶内酶切筛选减少样本的复杂性 325 Veronika Reisinger and Lutz A.Eichacker 19. 聚合物双水相系统逆流分配法分离神经系统质膜 335 Jens Schindler and Hans Gerd NothWang 20. 液相色谱串联质谱技术进行拟南芥蛋白质组分析的质膜蛋白富集和制备 341 Srijeet K.Mitra，Steven D.Clouse，and Michael B.Goshe 第八部分 蛋白质相互作用分析 21.Strep/FLAG(SF)-串联亲和纯化标签用于哺乳动物细胞蛋白质复合物串联亲和纯化 359 Christian Johannes Gloeckner，Karsten Boldt，Annette Schumacher，and Marius Ueffing 22. 顺序多肽亲和纯化系统分离和鉴定大肠杆菌蛋白质复合物 373 Mohan Babu，Gareth Butland，Oxana Pogoutse，Joyce Li，Jack F.Greenblatt，and AndreWEmili 23. 生物信息学方法分析蛋白质相互作用 401 Beate Kruger and Thomas Dandekar 索引 433 (宋凯 张春秀 译) Contents Preface. v Contributors. ix PART I INTRODUCTION 1. Introduction to Proteomics 3 Friedrich Lottspeich PART II ELECTROPHORETIC SEPARATIONS 2. High-Resolution Two-Dimensional Electrophoresis 13 Walter Weiss and Angelika Gorg 3. Non-classical 2-D Electrophoresis 33 Jacqueline Burre，Ilka Wittig，and Hermann Sch？gger 4. Protein Detection and Quantitation Technologies for Gel-Based Proteome Analysis 59 Walter Weiss，Florian Weiland，and Angelika Gorg PART III MASS SPECTROMETRY AND TANDEM MASS SPECTROMETRY APPLICATIONS 5. MALDI MS 85 Rainer Cramer 6. Capillary Electrophoresis Coupled to Mass Spectrometry for Proteomic Profiling of Human Urine and Biomarker Discovery 105 Petra Zurbig，Eric Schiffer，and Harald Mischak 7. A Newcomer’s Guide to Nano-Liquid-Chromatography of Peptides 123 Thomas Frohlich and Georg J. Arnold 8. Multidimensional Protein Identification Technology 143 Katharina Lohrig and Dirk Wolters 9. Characterization of Platelet Proteins Using Peptide Centric Proteomics 155 Oliver Simon，Stefanie Wortelkamp，and Albert Sickmann 10. Identification of the Molecular Composition of the 20S Proteasome of Mouse Intestine by High-Resolution Mass Spectrometric Proteome Analysis 173 Reinhold Weber，Regina Preywisch，Nikolay Youhnovski，Marcus Groettrup，and Michael Przybylski PART IV QUANTITATIVE PROTEOMICS 11. Liquid Chromatography-Mass Spectrometry-Based Quantitative Proteomics. 189 Michael W. Linscheid，Robert Ahrends，Stefan Pieper，and Andreas Kuhn 12. iTRAQ-Labeling of In-Gel Digested Proteins for Relative Quantification 207 Carla Schmidt and Henning Urlaub 13. Electrospray Mass Spectrometry for Quantitative Plasma Proteome Analysis 227 Hong Wang and Sam Hanash PART V INTERPRETATION OF MASS SPECTROMETRY DATA 14. Algorithms and Databases 245 Lennart Martens and Rolf Apweiler 15. Shotgun Protein Identification and Quantification by Mass Spectrometry 261 Bingwen Lu，Tao Xu，Sung Kyu Park，and John R. Yates III PART VI ANALYSIS OF PROTEIN MODIFICATIONS 16. Proteomics Identification of Oxidatively Modified Proteins in Brain 291 Rukhsana Sultana，Marzia Perluigi，and D. Allan Butterfield 17. Isotope-Labeling and Affinity Enrichment of Phosphopeptides for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry 303 Uma Kota，Ko-yi Chien，and Michael B. Goshe PART VII SUBCELLULAR PROTEOMICS 18. Organelle Proteomics：Reduction of Sample Complexity by Enzymatic In-Gel Selection of Native Proteins 325 Veronika Reisinger and Lutz A. Eichacker 19. Isolation of Plasma Membranes from the Nervous System by Countercurrent Distribution in Aqueous Polymer Two-Phase Systems 335 Jens Schindler and Hans Gerd Nothwang 20. Enrichment and Preparation of Plasma Membrane Proteins from Arabidopsis thaliana for Global Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry 341 Srijeet K. Mitra，Steven D. Clouse，and Michael B. Goshe PART VIII ANALYSIS OF PROTEIN INTERACTIONS 21. Tandem Affinity Purification of Protein Complexes from Mammalian Cells by the Strep/FLAG (SF)-TAP Tag 359 Christian Johannes Gloeckner，Karsten Boldt，Annette Schumacher，and Marius Ueffing 22. Sequential Peptide Affinity Purification System for the Systematic Isolation and Identification of Protein Complexes from Escherichia coli 373 Mohan Babu，Gareth Butland，Oxana Pogoutse，Joyce Li，Jack F. Greenblatt，and AndreWEmili 23. Bioinformatical Approaches to Detect and Analyze Protein Interactions. 401 Beate Kruger and Thomas Dandekar Index 433
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