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Proteomics

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Lucio Comai

    1. Keck School of Medicine, University of Southern California, Los Angeles, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Jonathan E. Katz

    1. Keck School of Medicine, University of Southern California, Los Angeles, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  3. Parag Mallick

    1. Stanford University, Palo Alto, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains keys notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1550)

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. A Robust Protocol for Protein Extraction and Digestion

    • Michelle Atallah, Mark R. Flory, Parag Mallick
    Pages 1-10

  3. Improving Proteome Coverage and Sample Recovery with Enhanced FASP (eFASP) for Quantitative Proteomic Experiments

    • Jonathan Erde, Rachel R. Ogorzalek Loo, Joseph A. Loo
    Pages 11-18

  4. Proteome Characterization of a Chromatin Locus Using the Proteomics of Isolated Chromatin Segments Approach

    • Sophie L. Kan, Nehmé Saksouk, Jérome Déjardin
    Pages 19-33

  5. Profiling Cell Lines Nuclear Sub-proteome

    • Aline Poersch, Andrea G. Maria, Camila S. Palma, Mariana L. Grassi, Daniele Albuquerque, Carolina H. Thomé et al.
    Pages 35-46

  6. Optimized Enrichment of Phosphoproteomes by Fe-IMAC Column Chromatography

    • Benjamin Ruprecht, Heiner Koch, Petra Domasinska, Martin Frejno, Bernhard Kuster, Simone Lemeer
    Pages 47-60

  7. Full Membrane Protein Coverage Digestion and Quantitative Bottom-Up Mass Spectrometry Proteomics

    • Joseph Capri, Julian P. Whitelegge
    Pages 61-67

  8. Hydrophilic Strong Anion Exchange (hSAX) Chromatography Enables Deep Fractionation of Tissue Proteomes

    • Benjamin Ruprecht, Dongxue Wang, Riccardo Zenezini Chiozzi, Li-Hua Li, Hannes Hahne, Bernhard Kuster
    Pages 69-82

  9. High pH Reversed-Phase Micro-Columns for Simple, Sensitive, and Efficient Fractionation of Proteome and (TMT labeled) Phosphoproteome Digests

    • Benjamin Ruprecht, Jana Zecha, Daniel P. Zolg, Bernhard Kuster
    Pages 83-98

  10. Multi-Lectin Affinity Chromatography for Separation, Identification, and Quantitation of Intact Protein Glycoforms in Complex Biological Mixtures

    • Sarah M. Totten, Majlinda Kullolli, Sharon J. Pitteri
    Pages 99-113

  11. Parallel Exploration of Interaction Space by BioID and Affinity Purification Coupled to Mass Spectrometry

    • Geoffrey G. Hesketh, Ji-Young Youn, Payman Samavarchi-Tehrani, Brian Raught, Anne-Claude Gingras
    Pages 115-136

  12. LUMIER: A Discovery Tool for Mammalian Protein Interaction Networks

    • Miriam Barrios-Rodiles, Jonathan D. Ellis, Benjamin J. Blencowe, Jeffrey L. Wrana
    Pages 137-148

  13. Dual-Color, Multiplex Analysis of Protein Microarrays for Precision Medicine

    • Solomon Yeon, Florian Bell, Michael Shultz, Grace Lawrence, Michael Harpole, Virginia Espina
    Pages 149-170

  14. Quantitative Proteomics Using SILAC

    • Kian Kani
    Pages 171-184

  15. Relative Protein Quantification Using Tandem Mass Tag Mass Spectrometry

    • Lichao Zhang, Joshua E. Elias
    Pages 185-198

  16. Pathway-Informed Discovery and Targeted Proteomic Workflows Using Mass Spectrometry

    • Caroline S. Chu, Christine A. Miller, Andy Gieschen, Steve M. Fischer
    Pages 199-221

  17. Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers

    • Birgit Schilling, Bradford W. Gibson, Christie L. Hunter
    Pages 223-233

  18. Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols

    • Minghui Li, Alexander Goncearenco, Anna R. Panchenko
    Pages 235-260

  19. Protein Micropatterning Assay: Quantitative Analysis of Protein–Protein Interactions

    • Gerhard J. Schütz, Julian Weghuber, Peter Lanzerstorfer, Eva Sevcsik
    Pages 261-270

  20. Designing Successful Proteomics Experiments

    • Daniel Ruderman
    Pages 271-288
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Keywords

About this book

This volume aims to provide protocols on a wide range of biochemical methods, analytical approaches, and bioinformatics tools developed to analyze the proteome. 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, Proteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Editors and Affiliations

  • Keck School of Medicine, University of Southern California, Los Angeles, USA

    Lucio Comai, Jonathan E. Katz

  • Stanford University, Palo Alto, USA

    Parag Mallick

Bibliographic Information

  • Book Title: Proteomics

  • Book Subtitle: Methods and Protocols

  • Editors: Lucio Comai, Jonathan E. Katz, Parag Mallick

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6747-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2017

  • Hardcover ISBN: 978-1-4939-6745-2Published: 11 February 2017

  • Softcover ISBN: 978-1-4939-8290-5Published: 09 June 2018

  • eBook ISBN: 978-1-4939-6747-6Published: 10 February 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 371

  • Number of Illustrations: 16 b/w illustrations, 48 illustrations in colour

  • Topics: Protein Science

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