Integrative Proteomics

452 Pages·2012·31.893 MB·English

by  H. Leung

INTEGRATIVE PROTEOMICS

Edited by Hon-Chiu Eastwood Leung
Integrative Proteomics
Edited by Hon-Chiu Eastwood Leung
Subject Editors: Tsz-Kwong Man and Ricardo J. Flores

Published by InTech
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First published February, 2012
Printed in Croatia

A free online edition of this book is available at www.intechopen.com
Additional hard copies can be obtained from [email protected]

Integrative Proteomics, Edited by Hon-Chiu Eastwood Leung;
Subject Editors: Tsz-Kwong Man and Ricardo J. Flores
p. cm.
ISBN 978-953-51-0070-6

Contents

Preface IX
Part 1 Proteomics – Historical Review 1
Chapter 1 Strategies for Protein Separation 3
Fernanda Salvato, Mayra Costa da Cruz Gallo de Carvalho
and Aline de Lima Leite
Chapter 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 45
Chapter 3 Proteomic Analyses of Cells
Isolated by Laser Microdissection 47
Valentina Fiorilli, Vincent P. Klink and Raffaella Balestrini
Chapter 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
Chapter 5 Simple and Rapid Proteomic Analysis
by Protease-Immobilized Microreactors 93
Hiroshi Yamaguchi, Masaya Miyazaki and Hideaki Maeda
Chapter 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 133
Chapter 7 Preparation of Protein Samples for
2-DE from Different Cotton Tissues 135
Chengjian Xie, Xiaowen Wang, Anping Sui and Xingyong Yang
VI Contents

Chapter 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 157
Chapter 9 Targeted High-Throughput
Glycoproteomics for Glyco-Biomarker Discovery 159
Eunju Choi and Michelle M. Hill
Chapter 10 Recent Advances in Glycosylation Modifications
in the Context of Therapeutic Glycoproteins 183
Xiaotian Zhong and Will Somers
Chapter 11 Detection of Protein Phosphorylation
by Open-Sandwich Immunoassay 197
Yuki Ohmuro-Matsuyama, Masaki Inagaki and Hiroshi Ueda
Chapter 12 Phosphoproteomics: Detection, Identification
and Importance of Protein Phosphorylation 215
Min Jia, Kah Wai Lin and Serhiy Souchelnytskyi
Chapter 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
Chapter 14 Dynamics of Protein Complexes
Tracked by Quantitative Proteomics 257
Séverine Boulon
Chapter 15 Proteomics Analysis of Kinetically Stable Proteins 281
Ke Xia, Marta Manning, Songjie Zhang and Wilfredo Colón
Chapter 16 Vinyl Sulfone:
A Multi-Purpose Function in Proteomics 301
F. Javier Lopez-Jaramillo, Fernando Hernandez-Mateo
and Francisco Santoyo-Gonzalez
Chapter 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
Chapter 18 Quantitative Proteomics Using
iTRAQ Labeling and Mass Spectrometry 347
H. R. Fuller and G. E. Morris
Contents VII

Chapter 19 Functional Proteomics:
Mapping Lipid-Protein Interactomes 363
Clive D’Santos and Aurélia E. Lewis
Chapter 20 Protein Thiol Modification and Thiol Proteomics 379
Yingxian Li, Xiaogang Wang and Qi Li
Part 5 Structural Proteomics 393
Chapter 21 The Utility of Mass Spectrometry
Based Structural Proteomics in
Biopharmaceutical Biologics Development 395
Parminder Kaur and Mark R. Chance
Part 6 Bioinformatics Tools 413
Chapter 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
Chapter 23 Application of Bioinformatics
Tools in Gel-Based Proteomics 425
Kah Wai Lin, Min Jia and Serhiy Souchelnytskyi

Preface

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