Introduction to Proteomics

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).

• Contributors xiPreface xv1 Introduction to Proteomics and Strategy for Protein Identification 1Jerzy Silberring2 Sample Preparation 7Agnieszka Kraj and Jerzy Silberring3 Chromatographic Separation Methods 133.1 Liquid Chromatography Linked to Mass Spectrometry 15Piotr Suder3.2 Multidimensional Liquid Chromatography Combined with Mass Spectrometry 23Anna Drabik4 Electrophoretic Separation Methods 314.1 One-Dimensional Gel Electrophoresis 33Anna Drabik and Piotr Laidler4.2 Two-Dimensional Gel Electrophoresis 43Anna Bierczynska-Krzysik and Gert Lubec5 Capillary Electrophoresis 55Marek Noga6 Protein Blotting 65Ibeth Guevara-Lora and Andrzej Kozik7 Introduction to Protein and Peptide Mass Spectrometry 777.1 Electrospray Ionization 79Piotr Suder7.2 Matrix-Assisted Laser Desorption/Ionization 89Agnieszka Kraj and Marcus Macht7.3 Imaging Mass Spectrometry 101Małgorzata Iwona Szynkowska and Jerzy Silberring7.4 Fragmentation and Sequencing in Proteomics 113Piotr Suder7.5 Protein Identification by Mass Spectrometry 123Anna Drabik, Marek Noga, Marcus Macht, and Jerzy Silberring7.6 Chemical Derivatization for Sequence Analysis 143Adam Moszczynski, Ulf Hellman, Tomasz Dylag, Marcus Macht, and Jerzy Silberring8 Protein Modifications 153Simone König9 Microfluidics 181Agnieszka Kraj and Jerzy Silberring10 Proteomics 18710.1 Quantitative Proteomics 189Tomasz Dylag, Anna Drabik, and Jerzy Silberring10.2 Structural Proteomics 199Małgorzata Rzychon10.3 Functional Proteomics 217Tomasz Dylag, Anna Drabik, and Adam Moszczynski10.4 Clinical Proteomics 233Anna Bodzon-Kulakowska11 Bioinformatics 247Pawel Ciborowski and Hesham AliAppendix A: Laboratory Exercises 275Anna Drabik, Anna Bierczynska-Krzysik, Anna Bodzon-Kulakowska, and Adam MoszczynskiAppendix B: Data Tables 293Appendix C: Internet Resources 299Filip Sucharski, Justyna Jarzebinska, and Hana RaoofIndex 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)