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Proteomics for Biomarker Discovery

  • Book
  • © 2013

Overview

Editors:
  1. Ming Zhou

    1. , Laboratory of Proteomics and Analytical, Frederick National Laboratory for Cancer, Frederick, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Timothy Veenstra

    1. , Laboratory of Proteomics and Analytical, Frederick National Laboratory for Cancer, Frederick, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols in the MiMB standard format
  • 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 1002)

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Table of contents (24 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis

    • Julian A. J. Jaros, Paul C. Guest, Sabine Bahn, Daniel Martins-de-Souza
    Pages 1-11

  3. Tissue Sample Preparation for Biomarker Discovery

    • Yoshiyuki Suehara, Daisuke Kubota, Tsuyoshi Saito
    Pages 13-23

  4. Subcellular Fractionation for Identification of Biomarkers: Serial Detergent Extraction by Subcellular Accessibility and Solubility

    • Sun-II Hwang, David K. Han
    Pages 25-35

  5. Analysis of Secreted Proteins

    • Valeria Severino, Annarita Farina, Angela Chambery
    Pages 37-60

  6. Preparation of Human Cerebrospinal Fluid for Proteomics Biomarker Analysis

    • Timothy J. Waybright
    Pages 61-70

  7. Proteomic Analysis of Frozen Tissue Samples Using Laser Capture Microdissection

    • Sumana Mukherjee, Jaime Rodriguez-Canales, Jeffrey Hanson, Michael R. Emmert-Buck, Michael A. Tangrea, DaRue A. Prieto et al.
    Pages 71-83

  8. Use of Formalin-Fixed, Paraffin-Embedded Tissue for Proteomic Biomarker Discovery

    • David B. Krizman, Jon Burrows
    Pages 85-92

  9. Phosphopeptide Enrichment Using Offline Titanium Dioxide Columns for Phosphoproteomics

    • Li-Rong Yu, Timothy Veenstra
    Pages 93-103

  10. iTRAQ-Labeling for Biomarker Discovery

    • Leroi V. DeSouza, Sébastien N. Voisin, K. W. Michael Siu
    Pages 105-114

  11. Analysis of Glycoproteins for Biomarker Discovery

    • Jintang He, Yashu Liu, Jing Wu, David M. Lubman
    Pages 115-122

  12. SILAC in Biomarker Discovery

    • Benjamin C. Orsburn
    Pages 123-131

  13. Trypsin-Mediated 18O/16O Labeling for Biomarker Discovery

    • Xiaoying Ye, King C. Chan, DaRue A. Prieto, Brian T. Luke, Donald J. Johann Jr., Luke H. Stockwin et al.
    Pages 133-149

  14. Two-Dimensional SDS-PAGE Fractionation of Biological Samples for Biomarker Discovery

    • Thierry Rabilloud, Sarah Triboulet
    Pages 151-165

  15. Informatics of Protein and Posttranslational Modification Detection via Shotgun Proteomics

    • Jerry D. Holman, Surendra Dasari, David L. Tabb
    Pages 167-179

  16. Quantitation of Met Tyrosine Phosphorylation Using MRM-MS

    • Zhaojing Meng, Apurva K. Srivastava, Ming Zhou, Timothy Veenstra
    Pages 181-193

  17. Preparation of Human Serum for Prolactin Measurement by Multiple Reaction Monitoring Mass Spectrometry

    • Timothy J. Waybright, Xia Xu, Jessica M. Faupel-Badger, Zhen Xiao
    Pages 195-203

  18. Label-Free Quantitative Shotgun Proteomics Using Normalized Spectral Abundance Factors

    • Karlie A. Neilson, Tim Keighley, Dana Pascovici, Brett Cooke, Paul A. Haynes
    Pages 205-222

  19. Employment of Complementary Dissociation Techniques for Body Fluid Characterization and Biomarker Discovery

    • David M. Good, Dorothea Rutishauser
    Pages 223-232

  20. Phosphopeptide Microarrays for Comparative Proteomic Profiling of Cellular Lysates

    • Liqian Gao, Hongyan Sun, Mahesh Uttamchandani, Shao Q. Yao
    Pages 233-251
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Keywords

About this book

With the advent of proteomics came the development of technologies, primarily mass spectrometry, which allowed high-throughput identification of proteins in complex mixtures.  While the mass spectrometer resides at the heart of proteomics, its ability to characterize biological samples is only as good as the sample preparation and data analysis tools used in any study.  In Proteomics for Biomarker Discovery, expert researchers in the field detail many of the methods which are now commonly used to study proteomics. These include methods and techniques include both label-free approaches and those that utilize stable isotopes incorporated both during cell growth or added via a chemical reaction once the proteome is extracted from the cell. 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 key tips on troubleshooting and avoiding known pitfalls.

 

 

Authoritative and practical, Proteomics for Biomarker Discovery seeks to aid scientists in the further study the different sample preparation and data analysis tools used in proteomics today.

Editors and Affiliations

  • , Laboratory of Proteomics and Analytical, Frederick National Laboratory for Cancer, Frederick, USA

    Ming Zhou, Timothy Veenstra

Bibliographic Information

  • Book Title: Proteomics for Biomarker Discovery

  • Editors: Ming Zhou, Timothy Veenstra

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-360-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2013

  • Hardcover ISBN: 978-1-62703-359-6Published: 27 April 2013

  • Softcover ISBN: 978-1-4939-5999-0Published: 23 August 2016

  • eBook ISBN: 978-1-62703-360-2Published: 15 June 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 320

  • Number of Illustrations: 23 b/w illustrations, 34 illustrations in colour

  • Topics: Protein Science, Proteomics

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