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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

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  • 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. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Introduction

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Survey of Shotgun Proteomics

      • Fabio Cesar Sousa Nogueira, Gilberto B. Domont
      Pages 3-23

  3. Sample Pre-fractionation

    1. Front Matter

      Pages 25-25
      Download chapter PDF

    2. LC-MALDI-TOF/TOF for Shotgun Proteomics

      • Patricia Fernández-Puente, Jesús Mateos, Francisco J. Blanco, Cristina Ruiz-Romero
      Pages 27-38

    3. Fully Automatable Multidimensional Reversed-Phase Liquid Chromatography with Online Tandem Mass Spectrometry

      • Maggie P. Y. Lam, Chun Hin Law, Quan Quan, Yun Zhao, Ivan K. Chu
      Pages 39-51

    4. GeLC-MS/MS Analysis of Complex Protein Mixtures

      • Monika Dzieciatkowska, Ryan Hill, Kirk C. Hansen
      Pages 53-66

    5. IPG Strip-Based Peptide Fractionation for Shotgun Proteomics

      • Murat Eravci, Christian Sommer, Matthias Selbach
      Pages 67-77

  4. In Vivo Stable Isotope Labeling

    1. Front Matter

      Pages 79-79
      Download chapter PDF

    2. SILAC Yeast: From Labeling to Comprehensive Proteome Quantification

      • Lyris M. F. de Godoy
      Pages 81-109

    3. Analysis of Proteome Dynamics in Mice by Isotopic Labeling

      • John C. Price, Sina Ghaemmaghami
      Pages 111-131

    4. Stable Isotope Labeling in Mammals (SILAM)

      • Daniel B. McClatchy, John R. Yates III
      Pages 133-146

    5. Analysis of Individual Protein Turnover in Live Animals on a Proteome-Wide Scale

      • Stefan Reckow, Christian Webhofer
      Pages 147-154

  5. In Vitro Stable Isotope Labeling

    1. Front Matter

      Pages 155-155
      Download chapter PDF

    2. Determining Protein Subcellular Localization in Mammalian Cell Culture with Biochemical Fractionation and iTRAQ 8-Plex Quantification

      • Andy Christoforou, Alfonso Martinez Arias, Kathryn S. Lilley
      Pages 157-174

    3. Brain Quantitative Proteomics Combining GeLC-MS and Isotope-Coded Protein Labeling (ICPL)

      • Giuseppina Maccarrone, Maria Lebar, Daniel Martins-de-Souza
      Pages 175-185

    4. Employing TMT Quantification in a Shotgun-MS Platform

      • Darragh P. O’Brien, John F. Timms
      Pages 187-199

    5. Employing TMT Quantification in Shotgun-MS Proteomic Analysis: A Focus on Skeletal Muscle

      • Bruno Menezes de Oliveira
      Pages 201-209

  6. Label-Free Proteomics

    1. Front Matter

      Pages 211-211
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    2. Spectral Counting Label-Free Proteomics

      • Liisa Arike, Lauri Peil
      Pages 213-222
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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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