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
Proteomics by means of mass spectrometry has rapidly changed the way that we analyze proteomes. Gel-Free Proteomics: Methods and Protocols addresses contemporary methods for gel-free proteome research with a special focus on differential analysis and protein modifications. Divided into twenty-five chapters, this detailed volume meticulously describes vital procedures needed to perform gel-free proteomics, ranging from sample preparation, isotope labeling for differential proteomics, enrichment technologies for modified proteins and peptides, and bioinformatics. 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.
Authoritative and easily accessible, Gel-Free Proteomics: Methods and Protocols serves as a timely resource for both professionals and novices pursuing research in this critical field.
