Quantitative Methods in 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, René Peiman Zahedi, and Albert Sickmann

9. Relative Protein Quantification by MS/MS Using the Tandem Mass Tag Technology

Loïc Dayon and Jean-Charles Sanchez

10. A Rapid Approach for Isobaric Peptide Termini Labeling (Rapid-IPTL)

Christian J. Koehler, Margnus Ø. 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 Stühler

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 Hüttemann, 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, André 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, René Peiman Zahedi, Lennart Martens, and Albert Sickmann

31. MSQuant: A Platform for Stable Isotope-Based Quantitative Proteomics

Joost W. Gouw and Jeroen Krijgsveld