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Shotgun Proteomics

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Daniel Martins-de-Souza

    1. Ludwig-Maximilians-University, Munich, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols involving a wide array of proteome studies
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1156)

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Table of contents (31 protocols)

  1. Label-Free Proteomics

    1. Quantification of Proteins by Label-Free LC-MSE

      • Alon Savidor, Yishai Levin
      Pages 223-236

  2. Proteomics Informatics and Quantitation

    1. Front Matter

      Pages 237-237
      Download chapter PDF

    2. Bioinformatics for Proteomics: Opportunities at the Interface Between the Scientists, Their Experiments, and the Community

      • Marc Vaudel, Harald Barsnes, Lennart Martens, Frode S. Berven
      Pages 239-248

  3. Protein–Protein Interactions

    1. Front Matter

      Pages 249-249
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    2. Identification of DNA Damage Checkpoint-Dependent Protein Interactions in Saccharomyces cerevisiae Using Quantitative Mass Spectrometry

      • Francisco M. Bastos de Oliveira, Marcus B. Smolka
      Pages 251-263

    3. Application of Shotgun Proteomics for Discovery-Driven Protein–Protein Interaction

      • Livia Goto-Silva, Zoltan Maliga, Mikolaj Slabicki, Jimmy Rodriguez Murillo, Magno Junqueira
      Pages 265-278

    4. Mapping Protein Complexes Using Covalently Linked Antibodies and Isobaric Mass Tags

      • Antje Dittmann, Sonja Ghidelli-Disse, Carsten Hopf, Marcus Bantscheff
      Pages 279-291

  4. Targeted Proteomics

    1. Front Matter

      Pages 293-293
      Download chapter PDF

    2. Biomarker Verification Using Selected Reaction Monitoring and Shotgun Proteomics

      • Angel Mauricio Castro-Gamero, Clarice Izumi, José César Rosa
      Pages 295-306

    3. Use of Universal Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-Based Selected Reaction Monitoring (SRM) Approach for Verification of Breast Cancer-Related Protein Markers

      • Ning Qing Liu, Lennard J. M. Dekker, Martijn M. Van Duijn, Arzu Umar
      Pages 307-322

    4. The Secretome Analysis by High-Throughput Proteomics and Multiple Reaction Monitoring (MRM)

      • Vitor M. Faça, Camila S. Palma, Daniele Albuquerque, Gabriela N. S. Canchaya, Mariana L. Grassi, Vera L. Epifânio et al.
      Pages 323-335

    5. Preparation of Heteroelement-Incorporated and Stable Isotope-Labeled Protein Standards for Quantitative Proteomics

      • Anna Konopka, Nico Zinn, Christina Wild, Wolf D. Lehmann
      Pages 337-363

  5. Posttranslational Modifications

    1. Front Matter

      Pages 365-365
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    2. One-Source Peptide/Phosphopeptide Ratio Standards for Accurate and Site-Specific Determination of the Degree of Phosphorylation

      • Martin E. Boehm, Bettina Hahn, Wolf D. Lehmann
      Pages 367-378

    3. Quantitative Glycoproteomics for N-Glycoproteome Profiling

      • Sheng Pan
      Pages 379-388

    4. A Practical Recipe to Survey Phosphoproteomes

      • William C. Edelman, Kelsey M. Haas, Joanne I. Hsu, Robert T. Lawrence, Judit Villén
      Pages 389-405

    5. Quantitation of the Phosphoproteome Using the Library-Assisted eXtracted Ion Chromatogram (LAXIC) Strategy

      • Justine V. Arrington, Liang Xue, W. Andy Tao
      Pages 407-416

    6. Fast, Efficient, and Quality-Controlled Phosphopeptide Enrichment from Minute Sample Amounts Using Titanium Dioxide

      • Clarissa Dickhut, Sonja Radau, René P. Zahedi
      Pages 417-430

    7. Quantifying Small Molecule-Induced Changes in Cellular Protein Expression and Posttranslational Modifications Using Isobaric Mass Tags

      • Isabelle Becher, Maria Fälth Savitski, Marcus Bantscheff
      Pages 431-443

  6. Mass Spectrometry for Protein Analysis

    1. Front Matter

      Pages 445-445
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Keywords

About this book

Shotgun Proteomics: Methods and Protocols serves as a vital collection of protocols through which thousands of proteins can be simultaneously identified, quantified and characterized in a high throughput manner. Beginning with the history of proteomics centered on the vital role of mass spectrometry in its development, this detailed volume continues with chapters on sample pre-fractionation, in vivo and in vitro stable isotope labeling, label-free proteomics, informatics, protein-protein interactions, targeted proteomics and post-translational modifications. Written for the highly successful Methods in Molecular Biology series, 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.

Practical and comprehensive, Shotgun Proteomics: Methods and Protocols is an ideal and up-to-date guide for researchers seeking to understand the proteome of any given species.

Editors and Affiliations

  • Ludwig-Maximilians-University, Munich, Germany

    Daniel Martins-de-Souza

Bibliographic Information

  • Book Title: Shotgun Proteomics

  • Book Subtitle: Methods and Protocols

  • Editors: Daniel Martins-de-Souza

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-0685-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2014

  • Hardcover ISBN: 978-1-4939-0684-0Published: 03 May 2014

  • Softcover ISBN: 978-1-4939-4695-2Published: 30 April 2017

  • eBook ISBN: 978-1-4939-0685-7Published: 02 May 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 492

  • Number of Illustrations: 33 b/w illustrations, 48 illustrations in colour

  • Topics: Protein Science, Proteomics

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