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Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine.
Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the 'hot' topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics.
Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. It is authoritative and easily accessible, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.
Part I. Planning a Proteomic Experiment
1. Important Issues in Planning a Proteomics Experiment - Statistical Considerations of Quantitative Proteomic Data Katharina Podwojski, Christian Stephan, and Martin Eisenacher
Part II. Quantitative Proteomics: Gel-Based Methods
2. The Whereabouts of 2D Gels in Quantitative Proteomics Thierry Rabilloud
3. Proteome Analysis with Classical 2D-PAGE Caroline May, Frederic Brosseron, Kathy Pfeiffer, Helmut E. Meyer, and Katrin Marcus
4. Fast and Sentitive Coomassie Staining in Quantitative Proteomics Nadine Dyballa and Sabine Metzger
5. Silver Staining of 2D Electrophoresis Gels Thierry Rabilloud
6. Differential Proteome Analysis using 2D-DIGE Caroline May, Frederic Brosseron, Piotr Chartowski, Helmut E. Meyer, and Katrin Marcus
Part III. Quantitative Proteomics: MS-Based Methods
7. Quantitative Mass Spectrometry-Based Proteomics: An Overview Miroslav Nikolov, Carla Schmidt, and Henning Urlaub
8. Robust Workflow for iTRAQ-Based Peptide and Protein Quantification Florian Beck, Julia Maria Burkhart, Joergt Geiger, Rene Peiman Zahedi, and Albert Sickmann
9. Relative Protein Quantification by MS/MS Using the Tandem Mass Tag Technology Loic Dayon and Jean-Charles Sanchez
10. A Rapid Approach for Isobaric Peptide Termini Labeling (Rapid-IPTL) Christian J. Koehler, Margnus O. Arntzen, Achim Treumann, and Bernd Thiede
11. ICPL - Isotope Coded Protein Label Josef Kellermann and Friedrich Lottspeich
12. Hydroponic Isotope Labeling of Entire Plants (HILEP) and High Performance Mass Spectrometry For Quantitative Plant Proteomics Laurence V. Bindschedler, Davinia J.S. Mills, and Rainer Cramer
13. In Vivo Quantitative Proteome Profiling: Planning and Evaluation of SILAC Experiments Marieluise Kirchner and Matthias Selbach
14. SILAC for the Study of Mammalian Cell Lines and Yeast Protein Complexes Heike Piechura, Silke Oeljeklaus, and Bettina Warscheid
15. Post-Digestion 18O Exchange/Labeling for Quantitative Shotgun Proteomics of Membrane Proteins Xiaoying Ye, Brian T. Luke, Donald J. Johann Jr, King C. Chan, DaRue A. Prieto, Akira Ono, Timothy D. Veenstra, and Josip Blonder
16. Application of Label Free Proteomics for Differential Analysis of Lung Carcinoma Cell Line A549 Barbara Sitek, Daniel Waldera, Gereon Poschmann, Helmut E. Meyer, and Kai Stuhler
17. Absolute Quantification (AQUA) of Proteins Using Standard Peptides and Multiple Reaction Monitoring (MRM) Carla Schmidt and Henning Urlaub
18. Absolute Multiplexed Protein Quantification Using QconCAT Technology Philip J. Brownridge, Victoria M. Harman, Deborah M. Simpson, and Robert K. Beynon
19. A Practical Guide to the FLEXIQuant Method Sasha Singh, Marc Kirchner, Judith Steen, and Hanno Steen
20. Label-Free Protein Quantitation Using Weighted Spectral Counting Christine Vogel and Edward M. Marcotte
Part IV. Specific Methods - Detection and Quantification of Post-Translational Modifications
21. Discovering the Phosphoproteome of the Hydrophobic Cytochrome c Oxidase Membrane Protein Complex Stefan Helling, Maik Huttemann, Bernhard Kadenbach, Rabia Ramzan, Sebastian Vogt, and Katrin Marcus
22. Assay - A Quantitative Mass Spectrometry-Based Approach for Kinase Client Screening and Activity Analysis Yadong Huang and Jay J. Thelen
23. Robust and High-Throughput Sample Preparation for (Semi-)Quantitative Analysis of N-Glycosylation Profiles from Plasma Samples L. Renee Ruhaak, Carolin Huhn, Carolien A. M. Koeleman, Andre M. Deelder, and Manfred Wuhrer
24. Quantitative Redox Proteomics - The NOxICAT Method Claudia Lindemann and Lars I. Leichert
25. Quantitative Analysis of S-Nitrosylated Proteins Federico Torta and Angela Bachi
26. Analysis of Ubiquitinated Proteome by Quantitative Mass Spectrometry Chan Hyun Na and Junmin Peng
27. Identification of Endogenous SUMO1 Accepter Sites by Mass Spectrometry He-Hsuan Hsiao, Erick Meulmeester, and Henning Urlaub
Part V. Data Analysis, Software Tools
28. Search and Decoy: the Automatic Identification of Mass Spectra Martin Eisenacher, Michael Kohl, Michael Turewicz, Markus-Hermann Koch, Julian Uszkoreit, and Christian Stephan
29. Software Tools for MS-Based Quantitative Proteomics - A Brief Overview Simone Lemeer, Hannes Hahne, Fiona Pachl, and Bernhard Kuster
30. iTRAQ Data Interpretation Marc Vaudel, Julia Maria Burkhart, Rene Peiman Zahedi, Lennart Martens, and Albert Sickmann
31. MSQuant: A Platform for Stable Isotope-Based Quantitative Proteomics Joost W. Gouw and Jeroen Krijgsveld
