Introduction to Proteomics

Introduction to Proteomics is written by seasoned researchers with years of practical experience. In addition to comprehensive discussions of the basic concepts, techniques, and applications of the subject, the text also includes an extensive glossary and a chapter containing laboratory exercises and protocols. While mass spectrometry is central to proteomics, the book discusses all of the analytical techniques a student is likely to need when faced with real-world problems, such as sample preparation, chromatographic and electrophoretic separation, micro-total analysis systems, and bioinformatics.

Contributors xi

Preface xv

1 Introduction to Proteomics and Strategy for Protein Identification 1
Jerzy Silberring

2 Sample Preparation 7
Agnieszka Kraj and Jerzy Silberring

3 Chromatographic Separation Methods 13

3.1 Liquid Chromatography Linked to Mass Spectrometry 15
Piotr Suder

3.2 Multidimensional Liquid Chromatography Combined with Mass Spectrometry 23
Anna Drabik

4 Electrophoretic Separation Methods 31

4.1 One-Dimensional Gel Electrophoresis 33
Anna Drabik and Piotr Laidler

4.2 Two-Dimensional Gel Electrophoresis 43
Anna Bierczynska-Krzysik and Gert Lubec

5 Capillary Electrophoresis 55
Marek Noga

6 Protein Blotting 65
Ibeth Guevara-Lora and Andrzej Kozik

7 Introduction to Protein and Peptide Mass Spectrometry 77

7.1 Electrospray Ionization 79
Piotr Suder

7.2 Matrix-Assisted Laser Desorption/Ionization 89
Agnieszka Kraj and Marcus Macht

7.3 Imaging Mass Spectrometry 101
Małgorzata Iwona Szynkowska and Jerzy Silberring

7.4 Fragmentation and Sequencing in Proteomics 113
Piotr Suder

7.5 Protein Identification by Mass Spectrometry 123
Anna Drabik, Marek Noga, Marcus Macht, and Jerzy Silberring

7.6 Chemical Derivatization for Sequence Analysis 143
Adam Moszczynski, Ulf Hellman, Tomasz Dylag, Marcus Macht, and Jerzy Silberring

8 Protein Modifications 153
Simone König

9 Microfluidics 181
Agnieszka Kraj and Jerzy Silberring

10 Proteomics 187

10.1 Quantitative Proteomics 189
Tomasz Dylag, Anna Drabik, and Jerzy Silberring

10.2 Structural Proteomics 199
Małgorzata Rzychon

10.3 Functional Proteomics 217
Tomasz Dylag, Anna Drabik, and Adam Moszczynski

10.4 Clinical Proteomics 233
Anna Bodzon-Kulakowska

11 Bioinformatics 247
Pawel Ciborowski and Hesham Ali

Appendix A: Laboratory Exercises 275
Anna Drabik, Anna Bierczynska-Krzysik, Anna Bodzon-Kulakowska, and Adam Moszczynski

Appendix B: Data Tables 293

Appendix C: Internet Resources 299
Filip Sucharski, Justyna Jarzebinska, and Hana Raoof

Index 305

"This work will be a useful tool for students of biotechnology, and it will also serve as an excellent reference for researchers interested in applying proteomics to their own investigations." (CHOICE, August 2009)

Agnieszka Kraj, PHD, is an Associate Professor of the Neurobiochemistry Department in the Faculty of Chemistry at Jagiellonian University, Poland.

Jerzy Silberring, PHD, is the Head of the Neurobiochemistry Department in the Faculty of Chemistry as well as the former deputy head of the Regional Laboratory for Physicochemical Analyses at Jagiellonian University, Poland. Dr. Silberring is coeditor of Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research and Mass Spectrometry: Instrumentation, Interpretation, and Applications (both from Wiley).

Everything you need to begin conducting your own proteomics research

Proteomics: Introduction to Methods and Applications is the ideal introduction to the field of proteomics, giving readers the skills and knowledge needed to study proteins, their structure, and their function in cells, tissues, and organisms. Written by experienced researchers, the text not only covers all the basic concepts, techniques, and applications, it also offers readers insights and practical tips based on the authors' many years of hands-on work in proteomics research. Moreover, the text has been carefully edited to ensure a thorough, consistent, and highly readable approach throughout all the chapters.

This text offers everything readers need to begin conducting their own proteomics research, including:

• A full chapter dedicated to laboratory exercises and protocols to help readers apply their skills

• Step-by-step explanations of key analytical methods, including mass spectrometry, sample preparation, chromatographic and electrophoretic separation, and micro-total analysis systems

• Complete coverage of bioinformatics, including an introduction to important proteomics databases

• A glossary defining the key terms in the field

• An appendix with an annotated list of Internet resources, information on post-translational modifications, and the masses and compositions of amino acid residues

This text is designed for upper-level undergraduate and graduate courses in proteomics. Upon successful completion of the text, students are able to apply their skills and knowledge to solve problems in such fields as biotechnology, drug discovery, and medical research.