Gel-Free Proteomics: Methods and Protocols

ISBN-13: 9781493958191 / Angielski / Miękka / 2016 / 400 str.

Kris Gevaert; Joel Vandekerckhove

Opis

Focusing on differential analysis and protein modifications, Gel-Free Proteomics addresses contemporary methods for gel-free proteome research. The text describes the vital procedures needed to perform gel-free proteomics.

Spis treści

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

            Giuseppe Palmisano, Sara E. Lendal, and Martin R. Larsen

 

22. Chemical de-O-Glycosylation of Glycoproteins for Applications in LC-based Proteomics

            Franz-Georg Hanisch

 

23. Ubiquitination and Degradation of Proteins

            Yelena Kravtsova-Ivantsiv and Aaron Ciechanover

 

24. Bioinformatics Challenges in Mass Spectrometry Driven Proteomics

            Lennart Martens

 

25. A Case Study on the Comparison of Different Software Tools for Automated Quantification of Peptides

            Niklaas Colaert, Joël Vandekerckhove, Lennart Martens, and Kris Gevaert

Blurb

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.