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Proteomics in Systems Biology

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. Jörg Reinders

    1. University of Regensburg Institute of Functional Genomics, Regensburg, Germany

    View editor publications

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1394)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines

    • Amanda Edwards, Wilhelm Haas
    Pages 1-13

  3. Sample Preparation Approaches for iTRAQ Labeling and Quantitative Proteomic Analyses in Systems Biology

    • Christos Spanos, J. Bernadette Moore
    Pages 15-24

  4. Two Birds with One Stone: Parallel Quantification of Proteome and Phosphoproteome Using iTRAQ

    • Fiorella A. Solari, Laxmikanth Kollipara, Albert Sickmann, René P. Zahedi
    Pages 25-41

  5. Selected Reaction Monitoring to Measure Proteins of Interest in Complex Samples: A Practical Guide

    • Yuehan Feng, Paola Picotti
    Pages 43-56

  6. Monitoring PPARG-Induced Changes in Glycolysis by Selected Reaction Monitoring Mass Spectrometry

    • Andreas Hentschel, Robert Ahrends
    Pages 57-74

  7. A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses

    • Annie Moradian, Tanya R. Porras-Yakushi, Michael J. Sweredoski, Sonja Hess
    Pages 75-85

  8. Targeted Phosphoproteome Analysis Using Selected/Multiple Reaction Monitoring (SRM/MRM)

    • Jun Adachi, Ryohei Narumi, Takeshi Tomonaga
    Pages 87-100

  9. Testing Suitability of Cell Cultures for SILAC-Experiments Using SWATH-Mass Spectrometry

    • Yvonne Reinders, Daniel Völler, Anja-K. Bosserhoff, Peter J. Oefner, Jörg Reinders
    Pages 101-108

  10. Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes

    • Philip Lössl, Andrea Sinz
    Pages 109-127

  11. Tissue MALDI Mass Spectrometry Imaging (MALDI MSI) of Peptides

    • Birte Beine, Hanna C. Diehl, Helmut E. Meyer, Corinna Henkel
    Pages 129-150

  12. Ethyl Esterification for MALDI-MS Analysis of Protein Glycosylation

    • Karli R. Reiding, Emanuela Lonardi, Agnes L. Hipgrave Ederveen, Manfred Wuhrer
    Pages 151-162

  13. Characterization of Protein N-Glycosylation by Analysis of ZIC-HILIC-Enriched Intact Proteolytic Glycopeptides

    • Gottfried Pohlentz, Kristina Marx, Michael Mormann
    Pages 163-179

  14. Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways

    • Julian H. M. Kwan, Andrew Emili
    Pages 181-187

  15. A Systems Approach to Understand Antigen Presentation and the Immune Response

    • Nadine L. Dudek, Nathan P. Croft, Ralf B. Schittenhelm, Sri H. Ramarathinam, Anthony W. Purcell
    Pages 189-209

  16. Profiling of Small Molecules by Chemical Proteomics

    • Kilian V. M. Huber, Giulio Superti-Furga
    Pages 211-218

  17. Generating Sample-Specific Databases for Mass Spectrometry-Based Proteomic Analysis by Using RNA Sequencing

    • Toni Luge, Sascha Sauer
    Pages 219-232

  18. A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science

    • Reinhard Turetschek, David Lyon, Getinet Desalegn, Hans-Peter Kaul, Stefanie Wienkoop
    Pages 233-243

  19. From Phosphoproteome to Modeling of Plant Signaling Pathways

    • Maksim Zakhartsev, Heidi Pertl-Obermeyer, Waltraud X. Schulze
    Pages 245-259

  20. Interpretation of Quantitative Shotgun Proteomic Data

    • Elise Aasebø, Frode S. Berven, Frode Selheim, Harald Barsnes, Marc Vaudel
    Pages 261-273
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Keywords

About this book

This volume presents an overview of contemporary quantitative proteomics methods along with instructions on data interpretation, while providing examples on how to implement proteomics into systems biology. 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.

Thorough and practical, Proteomics in Systems Biology: Methods and Protocols is a valuable resource for researchers who are interested in using proteomics techniques to help answer biological and medical questions.

Editors and Affiliations

  • University of Regensburg Institute of Functional Genomics, Regensburg, Germany

    Jörg Reinders

About the editor

Dr. Joerg Reinders Institute of Functional Genomics University Regensburg Joseph-Engert-Strasse 9 93053 Regensburg Germany Phone: +49 941 943 5004 Fax: +49 941 943 5019 E-Mail: joerg.reinders@klinik.uni-regensburg.de

Bibliographic Information

  • Book Title: Proteomics in Systems Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Jörg Reinders

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3341-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3339-6Published: 23 December 2015

  • Softcover ISBN: 978-1-4939-8025-3Published: 27 March 2019

  • eBook ISBN: 978-1-4939-3341-9Published: 23 December 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 313

  • Number of Illustrations: 15 b/w illustrations, 61 illustrations in colour

  • Topics: Protein Science, Proteomics

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