Mass Spectrometry of Proteins

1. Front Matter

   Pages i-xiii

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2. New Biological Insights from Technological Breakthroughs

   1. Front Matter

      Pages 1-1

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   2. Next Generation Proteomics for Clinical Biomarker Detection Using SWATH-MS

      • Qifeng Lin, Hwee Tong Tan, Maxey C. M. Chung

      Pages 3-15

   3. A Combined Chemical Derivatization/Mass Spectrometric Method for the Enhanced Detection and Relative Quantification of Protein Ubiquitination

      • Navin Chicooree, John R. Griffiths

      Pages 17-24

   4. Assessment of Ubiquitin Chain Topology by Targeted Mass Spectrometry

      • Joseph Longworth, Gunnar Dittmar

      Pages 25-34

   5. Quantitative Phosphoproteomic Using Titanium Dioxide Micro-Columns and Label-Free Quantitation

      • Martin E. Barrios-Llerena, Thierry Le Bihan

      Pages 35-42

   6. Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond

      • Peder J. Lund, Yekaterina Kori, Xiaolu Zhao, Simone Sidoli, Zuo-Fei Yuan, Benjamin A. Garcia

      Pages 43-70

   7. Quantitative Analysis of Protein S-Acylation Site Dynamics Using Site-Specific Acyl-Biotin Exchange (ssABE)

      • Keith T. Woodley, Mark O. Collins

      Pages 71-82

   8. Reducing Complexity? Cysteine Reduction and S-Alkylation in Proteomic Workflows: Practical Considerations

      • Caroline A. Evans

      Pages 83-97

   9. Detection of Unknown Chemical Adduct Modifications on Proteins: From Wet to Dry Laboratory

      • Paola Antinori, Théo Michelot, Pierre Lescuyer, Markus Müller, Adelina E. Acosta-Martin

      Pages 99-113

   10. Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry

       • Joel D. Federspiel, Ileana M. Cristea

       Pages 115-143

   11. Metaproteomics of Freshwater Microbial Communities

       • David A. Russo, Narciso Couto, Andrew P. Beckerman, Jagroop Pandhal

       Pages 145-155

3. Dealing with Proteomics Data in a Big Data Era

   1. Front Matter

      Pages 157-157

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   2. Peptide-to-Protein Summarization: An Important Step for Accurate Quantification in Label-Based Proteomics

      • Martina Fischer, Thilo Muth, Bernhard Y. Renard

      Pages 159-180

   3. Experimental Design in Quantitative Proteomics

      • Tomasz Burzykowski, Jürgen Claesen, Dirk Valkenborg

      Pages 181-197

   4. Practical Integration of Multi-Run iTRAQ Data

      • Dana Pascovici, Xiaomin Song, Jemma Wu, Thiri Zaw, Mark Molloy

      Pages 199-215

   5. Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities

      • Andrew F. Jarnuczak, Tobias Ternent, Juan Antonio Vizcaíno

      Pages 217-235

   6. Computational Proteomics with Jupyter and Python

      • Lars Malmström

      Pages 237-248

   7. 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 et al.

      Pages 249-261

4. Back Matter

   Pages 263-264

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New insights into modern medicine and systems biology are enabled by innovative protocols and advanced technologies in mass spectrometry-based proteomics. This volume details new pipelines, workflows, and ways to process data that allow for new frontiers in proteomics to be pushed forward. With applications to biomarker discovery, interactions between proteins, between biological systems, dynamics of post-translational modifications among others, new protocols have been developed and iteratively refined to probe the endless complexity of the proteome in ever greater details. This volume deals with methods for data dependent and data independent mass spectrometry analyses. Valuable, first-hand information is provided from designing experiments, sample preparation and analysis, exploitation of public datasets and carrying out reproducible data pipelines, using modern computational tools such as Galaxy or Jupyter. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 



Authoritative and cutting-edge, Mass Spectrometry of Proteins: Methods and Protocols aims to ensure successful results in the further study of this vital field. 

• iTRAQ
• TMT
• di methyl labelling
• QConCat
• quantitative proteomics

• Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK

  Caroline A. Evans

• Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, UK

  Phillip C. Wright

• Laboratoire GBCM (EA4627), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France

  Josselin Noirel

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