Mass Spectrometry of Proteins: Methods and Protocols

ISBN-13: 9781493992348 / Angielski / Miękka / 2020 / 264 str.

Caroline A. Evans;Phillip C. Wright;Josselin Noirel

Opis

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.

Spis treści

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, Théo Michelot, Pierre Lescuyer, Markus Müller, 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, Jürgen 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 Vizcaíno

15. Computational Proteomics with Jupyter and Python
Lars Malmström

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