Proteomic Profiling: Methods and Protocols

ISBN-13: 9781493925490 / Angielski / Twarda / 2015 / 501 str.

Anton Posch

Opis

This volume presents the latest developments of the main pillars of protein analysis, such as sample preparation, separation and characterization. The book begins by describing basic but important sample preparation protocols. It then goes on to describe more sophisticated procedures on enriching specific protein classes and concludes with detailed descriptions of integrated work-flows for comprehensive protein analysis and characterization. The authors of the individual chapters are renowned protein biochemists who have all set value to provide a detailed representation of their lab work. Throughout the chapters, these authors share important tips and tricks for a successful and reproducible employment of their protocols in other laboratories. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls.Authoritative and cutting-edge, Proteomic Profiling: Methods and Protocols is the perfect guide for students of Biochemistry, Biomedicine, Biology, and Genomics and will be an invaluable source for the experienced, practicing scientists.

Spis treści

1. Mechanical/Physical Methods of Cell Disruption and Tissue Homogenization
Stanley Goldberg

2. Sample Preservation Through Heat Stabilization of Proteins: Principles and Examples
Mats Borén

3. Isolating Peripheral Lymphocytes by Density Gradient Centrifugation and Magnetic Cell Sorting
Frederic Brosseron, Katrin Marcus, and Caroline May

4. Investigating the Adipose Tissue Secretome: A Protocol to Generate High Quality Samples Appropriate for Comprehensive Proteomic Profiling
Simon Göddeke, Jorg Kotzka, and Stefan Lehr

5. Methods for Proteomics-Based Analysis of the Human Muscle Secretome Using an in vitro Exercise Model
Mika Scheler, Martin Hrabě de Angelis, Hadi Al-Hasani, Hans-Ulrich Häring, Cora Weigert, and Stefan Lehr

6. Urinary Pellet Sample Preparation for Shotgun Proteomic Analysis of Microbial Infection and Host Pathogen Interactions
Yanbao Yu and Rembert Pieper

7. A Protocol for the Parallel Isolation of Intact Mitochondria from Rat Liver, Kidney, Heart and Brain
Sabine Schulz, Josef Lichtmannegger, Sabine Schmitt, Christin Leitzinger, Carola Eberhagen, Claudia Einer, Julian Kerth, Michaela Aichler, and Hans Zischka

8. Isolation of Mitochondria from Cultured Cells and Liver Tissue Biopsies for Molecular and Biochemical Analyses
Sabine Schmitt, Carola Eberhagen, Susanne Weber, Michaela Aichler, and Hans Zischka

9. Dynamic Range Compression with ProteoMiner^TM: Principles and Examples
Lei Li

10. Qualitative and Quantitative Proteomic Analysis of Formalin-Fixed Paraffin-Embedded (FFPE) Tissue
Omid Azimzadeh, Michael J. Atkinson, and Soile Tapio

11. Full-Length Protein Extraction Protocols and Gel-Based Downstream Applications in Formalin-Fixed Tissue Proteomics
Alessandro Tanca, Sergio Uzzau, and Maria Filippa Addis

12. Enrichment of Low-Abundant Protein Targets by Immunoprecipitation Upstream of Mass Spectrometry
Barbara Kaboord, Suzanne Smith, Bhavin Patel, and Scott Meier

13. Principles of Protein Labeling Techniques
Christian Obermaier, Anja Griebel, and Reiner Westermeier

14. Isolation of Extracellular Vesicles for Proteomic Profiling
Dong-Sic Choi and Yong Song Gho

15. A Protocol for Exosome Isolation and Characterization: Evaluation of Ultracentrifugation, Density-Gradient Separation, and Immunoaffinity Capture Methods
David W. Greening, Rong Xu, Hong Ji, Bow J. Tauro, and Richard J. Simpson

16. Chloroplast Isolation and Affinity Chromatography for Enrichment of Low Abundant Proteins in Complex Proteomes
Roman G. Bayer, Simon Stael, and Markus Teige

17. Depletion of RuBisCO Protein Using the Protamine Sulfate Precipitation Method  
Ravi Gupta and Sun Tae Kim

18. Step by Step Preparation of Proteins for Mass Spectrometric Analysis
Thomas Franz and Xinping Li

19. Identification of Protein N-Termini Using TMPP or Dimethyl Labeling and Mass Spectrometry
Jingjing Deng, Guoan Zhang, Fang-ke Huang, and Thomas A. Neubert

20. Optimization of Cell Lysis and Protein Digestion Protocols for Protein Analysis by LC-MS/MS
Dominic Winter, Alireza Dehghani, and Hanno Steen

21. Comprehensive Protocol to Simultaneously Study Protein Phosphorylation, Acetylation and N-Linked Sialylated Glycosylation
Marcella Nunes Melo-Braga, María Ibáñez-Vea, Martin Røssel Larsen, and Katarzyna Kulej

22. Protein Profiling and Phosphoprotein Analysis by Isoelectric Focusing
Giuseppina Maccarrone and Michaela D. Filiou

23. Principles and Examples of Gel-Based Approaches for Phosphoprotein Analysis
Birgit Steinberger and Corina Mayrhofer

24. Neutral Phosphate-Affinity SDS-PAGE System for Profiling of Protein Phosphorylation
Emiko Kinoshita-Kikuta, Eiji Kinoshita, and Tohru Koike

25. Enrichment and Identification of Bacterial Glycopeptides by Mass Spectrometry
Nichollas E. Scott and Stuart J. Cordwell

26. In-Gel Peptide IEF Sample Preparation for LC/MS Analysis
Thomas Berkelman, Sricharan Bandhakavi, and Aran Paulus

27. Western Blotting Using In-Gel Protein Labeling as a Normalization Control: Stain-Free Technology
Jennifer E. Gilda and Aldrin V. Gomes

28. 2-D Western Blotting for Evaluation of Antibodies Developed for Detection of Host Cell Protein
Tom Berkelman, Adriana Harbers, and Sricharan Bandhakavi

29. Free Flow Electrophoresis for Separation of Native Membrane Protein Complexes
Lutz Andreas Eichacker, Gerhard Weber, Ute Sukop-Köppel, and Robert Wildgruber

30. Three-Dimensional Electrophoresis for Quantitative Profiling of Complex Proteomes
Sergio Mauro, Bertrand Colignon, Marc Dieu, Edouard Delaive, and Martine Raes

31. A Bead-Based Multiplex Sandwich Immunoassay to Assess the Abundance and Posttranslational Modification State of β-Catenin
Nicola Groll, Cornelia Sommersdorf, Thomas O. Joos, and Oliver Poetz

32. Identification of SUMO E3 Ligase Specific Substrates Using the HuProt Human Proteome Microarray
Eric Cox, Ijeoma Uzoma, Catherine Guzzo, Jun Seop Jeong, Michael Matunis, Seth Blackshaw, and Heng Zhu

33. Amyloid-Binding Proteins: Affinity Based Separation, Proteomic Identification and Optical Biosensor Validation
Alexei Medvedev, Olga Buneeva, Arthur Kopylov, Oksana Gnedenko, Alexis Ivanov, Victor Zgoda, and A. A. Makarov 

34. Proteomic Profiling by Nanomaterials-Based Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for High-Resolution Data and Novel Protein Information Directly from Biological Samples
Suresh Kumar Kailasa and Hui-Fen Wu

O autorze

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