1. Mass Spectrometry-driven Proteomics: An Introduction

Kenny Helsens, Lennart Martens, Joël Vandekerckhove, and Kris Gevaert

2. Metabolic Labeling of Model Organisms using Heavy Nitrogen (15N)

Joost W. Gouw, Bastiaan B.J. Tops, and Jeroen Krijgsveld

3. Trypsin-catalyzed Oxygen-18 Labeling for Quantitative Proteomics

Brianne O. Petritis, Carrie D. Nicora, Wei-Jun Qian, and Richard D. Smith

4. ICPL Labeling Strategies for Proteome Research

Friedrich Lottspeich and Josef Kellermann

5. Quantitative Proteome Analysis using Isobaric Peptide Termini Labeling (IPTL)

Magnus Ø. Arntzen, Christian J. Koehler, Achim Treumann, and Bernd Thiede

6. Complete Chemical Modification of Amine and Acid Functional Groups of Peptides and Small Proteins

Casey J. Krusemark, Brian L. Frey, Lloyd M. Smith, and Peter J. Belshaw

7. Production and Use of Stable-isotope-labeled Proteins for Absolute Quantitative Proteomics

Dorothée Lebert, Alain Dupuis, Jérôme Garin, Christophe Bruley, and Virginie Brun

8. Organelle Proteomics

Sophie Duclos and Michel Desjardins

9. Membrane Protein Digestion - Comparison of LPI Hexalane with Traditional Techniques

Ping Sui, Tasso Miliotis, Max Davidson, Roger Karlsson, and Anders Karlsson

10. GeLCMS for In-depth Protein Characterization and Advanced Analysis of Proteomes

Alicia Lundby and Jesper V. Olsen

11. Exploring New Proteome Space: Combining Lys-N Proteolytic Digestion and Strong Cation Exchange (SCX) Separation in Peptide Centric MS-driven Proteomics

Nadia Taouatas, Shabaz Mohammed, and Albert J.R. Heck

12. Quantitation of Newly Synthesized Proteins by Pulse-labeling with Azidohomoalanine

Gertjan Kramer, Piotr T. Kasper, Luitzen de Jong, and Chris G. de Koster

13. Analytical Strategies in Mass Spectrometry Based Phosphoproteomics

Heidi Rosenqvist, Juanying Ye, and Ole N. Jensen

14. A Protocol on the Use of Titanium Dioxide Chromatography for Phosphoproteomics

Martijn W. H. Pinkse, Simone Lemeer, and Albert J.R. Heck

15. Positional Proteomis at the N-terminus as a Means of Proteome Simplification

Gemma R. Davidson, Stuart D. Armstrong, and Robert J. Beynon

16. N-terminomics: A High-content Screen for Protease Substrates and their Cleavage Sites

John C. Timmer and Guy S. Salvesen

17. Protease Specificity Profiling by Tandem Mass Spectrometry Using Proteome-derived Peptide Libraries

Oliver Schilling, Ulrich auf dem Keller, and Christopher M. Overall

18. Identification of Proteolytic Products and Natural Protein N-termini by Terminal Amine Isotopic Labeling of Substrates (TAILS)

Alain Doucet, Oded Kleifeld, Jayachandran N. Kizhakkedathu, and Christopher M. Overall

19. Lectins as Tools to Select for Glycosylated Proteins

Els J. M. Van Damme

20. Strong Cation Exchange Chromatography for Analysis of Sialylated Glycopeptides

Katharina Lohrig, Albert Sickmann, and Urs Lewandrowski

21. Titanium Dioxide Enrichment of Sialic Acid-containing Glycopeptides