Open Access Medical Books

INTEGRATIVE PROTEOMICS

TEXTBOOK : INTEGRATIVE PROTEOMICS

Edited by Hon-Chiu Eastwood Leung .

452 pages .
Open Access .
ISBN 978-953-51-0070-6 .


Proteomics has come of age. Two-dimensional gel electrophoresis (2D gel) was first used in the 1970s. With the advent of the human genome sequence and associated bioinformatics tools, and the advancement on protein separation and mass spectrometry in the 1990s and 2000s, the field Proteomics blossomed. The past decade has witnessed the development of clinical proteomics studies and fine tuning of proteomics studies to focus on a subset of proteome that are related to a biological phenotype. The rigorous bioinformatics standards developed along the way helped the data across platforms to be more compatible with each other.
The goal of this book is to provide insights for a broad audience base ranging from those who are new to those who are more experienced in the field of proteomics. This book covers the historical overview of proteomics, sample preparations, 2D gel separation of complex proteomes and associated databases, structural proteomics, and subproteome analyses with focus on i) glycoproteome, ii) phosphor-proteome, iii) protein:protein interactions, and iv) sub-proteomes captured by specific chemical groups. Surely, the data generated in the field of proteomics will only be making sense by the corresponding development of bioinformatics tools. The chapters in the section of bioinformatics will also touch on the pathway generation from the proteomics data.
Finally, I would like to thank the authors for sharing their experience within the chapters and to express my gratitude to Martina Durovic for the wonderful administrative assistance. Last but not least, I would like to thank the staff for taking the final steps to bring this publication to reality.


Hon-Chiu Eastwood Leung, Ph.D.
Assistant Professor, 
Baylor College of Medicine,
Houston, Texas,
USA
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CONTENTS : 


Part 1 Proteomics – Historical Review .


1 Strategies for Protein Separation 3 Fernanda Salvato, Mayra Costa da Cruz Gallo de Carvalho and Aline de Lima Leite

 2 Evolution of Proteomic Methods for Analysis of Complex Biological Samples – Implications for Personalized Medicine 29 Amanda Nouwens and Stephen Mahler


Part 2 Sample Preparation .


 3 Proteomic Analyses of Cells Isolated by Laser Microdissection 47 Valentina Fiorilli, Vincent P. Klink and Raffaella Balestrini

 4 A Critical Review of Trypsin Digestion for LC-MS Based Proteomics 73 Hanne Kolsrud Hustoft, Helle Malerod, Steven Ray Wilson, Leon Reubsaet, Elsa Lundanes and Tyge Greibrokk

 5 Simple and Rapid Proteomic Analysis by Protease-Immobilized Microreactors 93 Hiroshi Yamaguchi, Masaya Miyazaki and Hideaki Maeda

 6 Labeling Methods in Mass Spectrometry Based Quantitative Proteomics 111 Karen A. Sap and Jeroen A. A. Demmers


Part 3 2D Gel Electrophoresis and Databases .


 7 Preparation of Protein Samples for 2-DE from Different Cotton Tissues 135 Chengjian Xie, Xiaowen Wang, Anping Sui and Xingyong Yang

 8 2D-PAGE Database for Studies on Energetic Metabolism of the Denitrifying Bacterium Paracoccus denitrificans 141 Pavel Bouchal, Robert Stein, Zbyněk Zdráhal, Peter R. Jungblut and Igor Kučera


Part 4 Subproteomes Analyses .


 9 Targeted High-Throughput Glycoproteomics for Glyco-Biomarker Discovery 159 Eunju Choi and Michelle M. Hill

 10 Recent Advances in Glycosylation Modifications in the Context of Therapeutic Glycoproteins 183 Xiaotian Zhong and Will Somers

 11 Detection of Protein Phosphorylation by Open-Sandwich Immunoassay 197 Yuki Ohmuro-Matsuyama, Masaki Inagaki and Hiroshi Ueda

 12 Phosphoproteomics: Detection, Identification and Importance of Protein Phosphorylation 215 Min Jia, Kah Wai Lin and Serhiy Souchelnytskyi

 13 Proteome Kinetics: Coupling the Administration of Stable Isotopes with Mass Spectrometry-Based Analyses 233 Stephen F. Previs, Haihong Zhou, Sheng-Ping Wang, Kithsiri Herath, Douglas G. Johns, Thomas P. Roddy, Takhar Kasumov and Brian K. Hubbard

 14 Dynamics of Protein Complexes Tracked by Quantitative Proteomics 257 Séverine Boulon

 15 Proteomics Analysis of Kinetically Stable Proteins 281 Ke Xia, Marta Manning, Songjie Zhang and Wilfredo Colón

 16 Vinyl Sulfone: A Multi-Purpose Function in Proteomics 301 F. Javier Lopez-Jaramillo, Fernando Hernandez-Mateo and Francisco Santoyo-Gonzalez

 17 Gel-Free Proteome Analysis Isotopic Labelling Vs. Label-Free Approaches for Quantitative Proteomics 327 Baptiste Leroy, Nicolas Houyoux, Sabine Matallana-Surget and Ruddy Wattiez

 18 Quantitative Proteomics Using iTRAQ Labeling and Mass Spectrometry 347 H. R. Fuller and G. E. Morris

 19 Functional Proteomics: Mapping Lipid-Protein Interactomes 363 Clive D’Santos and Aurélia E. Lewis

 20 Protein Thiol Modification and Thiol Proteomics 379 Yingxian Li, Xiaogang Wang and Qi Li


Part 5 Structural Proteomics .


 21 The Utility of Mass Spectrometry Based Structural Proteomics in Biopharmaceutical Biologics Development 395 Parminder Kaur and Mark R. Chance


Part 6 Bioinformatics Tools .


 22 nwCompare and AutoCompare Softwares for Proteomics and Transcriptomics Data Mining – Application to the Exploration of Gene Expression Profiles of Aggressive Lymphomas 415 Fréderic Pont, Marie Tosolini, Bernard Ycart and Jean-Jacques Fournié

 23 Application of Bioinformatics Tools in Gel-Based Proteomics 425 Kah Wai Lin, Min Jia and Serhiy Souchelnytskyi .





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