Mass Spectrometry of Proteins: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

Part I New Biological Insights from Technological Breakthroughs

1. Next Generation Proteomics for Clinical Biomarker Detection using SWATH-MS
Qifeng Lin, Hwee Tong Tan, and Maxey C. M. Chung

2. A Combined Chemical Derivatization/Mass Spectrometric Method for the Enhanced Detection and Relative Quantification of Protein Ubiquitination
Navin Chicooree and John R. Griffiths

3. Assessment of Ubiquitin Chain Topology by Targeted Mass Spectrometry
Joseph Longworth and Gunnar Dittmar

4. Quantitative Phosphoproteomic using Titanium Dioxide Micro-Columns and Label Free Quantitation
Martin E. Barrios-LLerena and Thierry Le Bihan

5. Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond
Peder J. Lund, Yekaterina Kori, Xiaolu Zhao, Simone Sidoli, Zuo-Fei Yuan, and Benjamin A. Garcia

6. Quantitative Analysis of Protein S-Acylation Site Dynamics Using Site-Specific Acyl-Biotin Exchange (ssABE)
Keith T. Woodley and Mark O. Collins

7. Reducing Complexity? Cysteine Reduction and S-alkylation in Proteomic Workflows: Practical Considerations
Caroline A. Evans

8. Detection of Unknown Chemical Adduct Modifications on Proteins: From Wet to Dry Laboratory
Paola Antinori, Th?o Michelot, Pierre Lescuyer, Markus M?ller, and Adelina E. Acosta-Martin

9. Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry
Joel D. Federspiel and Ileana M. Cristea

10. Metaproteomics of Freshwater Microbial Communities
David A. Russo, Narciso Couto, Andrew P. Beckerman, and Jagroop Pandhal

Part II Dealing with Proteomics Data in a Big Data Era

11. Peptide-to-Protein Summarization: An Important Step for Accurate Quantification In Label-Based Proteomics
Martina Fischer, Thilo Muth, and Bernhard Y. Renard

12. Experimental Design in Quantitative Proteomics
Tomasz Burzykowski, J?rgen Claesen, and Dirk Valkenborg

13. Practical Integration of Multi-Run iTRAQ Data
Dana Pascovici, Xiaomin Song, Jemma Wu, Thiri Zaw, and Mark Molloy

14. Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities
Andrew F. Jarnuczak, Tobias Ternent, and Juan Antonio Vizca?no

15. Computational Proteomics with Jupyter and Python
Lars Malmstr?m

16. The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis
Paul A. Stewart, Brent M. Kuenzi, Subina Mehta, Praveen Kumar, James E. Johnson, Pratik Jagtap, Timothy J. Griffin, and Eric B. Haura