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Proteomics for Biomarker Discovery

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Virginie Brun

    1. Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France

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  2. Yohann Couté

    1. Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1959)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xii
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  2. Pre- and Post-analytical Factors in Biomarker Discovery

    • Frank Klont, Peter Horvatovich, Natalia Govorukhina, Rainer Bischoff
    Pages 1-22

  3. Pre-fractionation of Noncirculating Biological Fluids to Improve Discovery of Clinically Relevant Protein Biomarkers

    • Annarita Farina
    Pages 23-37

  4. Serum Exosome Isolation by Size-Exclusion Chromatography for the Discovery and Validation of Preeclampsia-Associated Biomarkers

    • Rosana Navajas, Fernando J. Corrales, Alberto Paradela
    Pages 39-50

  5. Protein Biomarker Discovery Using Human Blood Plasma Microparticles

    • Raghda Saad Zaghloul Taleb, Pacint Moez, Doreen Younan, Martin Eisenacher, Matthias Tenbusch, Barbara Sitek et al.
    Pages 51-64

  6. A Standardized and Reproducible Proteomics Protocol for Bottom-Up Quantitative Analysis of Protein Samples Using SP3 and Mass Spectrometry

    • Christopher S. Hughes, Poul H. Sorensen, Gregg B. Morin
    Pages 65-87

  7. Analyzing Cerebrospinal Fluid Proteomes to Characterize Central Nervous System Disorders: A Highly Automated Mass Spectrometry-Based Pipeline for Biomarker Discovery

    • Antonio Núñez Galindo, Charlotte Macron, Ornella Cominetti, Loïc Dayon
    Pages 89-112

  8. Lys-C/Trypsin Tandem-Digestion Protocol for Gel-Free Proteomic Analysis of Colon Biopsies

    • Armin Schniers, Yvonne Pasing, Terkel Hansen
    Pages 113-122

  9. Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics

    • Leslie Muller, Luc Fornecker, Sarah Cianferani, Christine Carapito
    Pages 123-127

  10. Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry

    • Alexandra Kraut, Mathilde Louwagie, Christophe Bruley, Christophe Masselon, Yohann Couté, Virginie Brun et al.
    Pages 129-150

  11. Discovering Protein Biomarkers from Clinical Peripheral Blood Mononuclear Cells Using Data-Independent Acquisition Mass Spectrometry

    • Xin Ku, Wei Yan
    Pages 151-161

  12. Intact Protein Analysis by LC-MS for Characterizing Biomarkers in Cerebrospinal Fluid

    • Jérôme Vialaret, Sylvain Lehmann, Christophe Hirtz
    Pages 163-172

  13. Detection of Proteoforms Using Top-Down Mass Spectrometry and Diagnostic Ions

    • Didia Coelho Graça, Ralf Hartmer, Wolfgang Jabs, Alexander Scherl, Lorella Clerici, Kaveh Samii et al.
    Pages 173-183

  14. Development of a Highly Multiplexed SRM Assay for Biomarker Discovery in Formalin-Fixed Paraffin-Embedded Tissues

    • Carine Steiner, Pierre Lescuyer, Jean-Christophe Tille, Paul Cutler, Axel Ducret
    Pages 185-203

  15. Development and Validation of Multiple Reaction Monitoring (MRM) Assays for Clinical Applications

    • Georgia Kontostathi, Manousos Makridakis, Vasiliki Bitsika, Nikolaos Tsolakos, Antonia Vlahou, Jerome Zoidakis
    Pages 205-223

  16. Protein-Level Statistical Analysis of Quantitative Label-Free Proteomics Data with ProStaR

    • Samuel Wieczorek, Florence Combes, Hélène Borges, Thomas Burger
    Pages 225-246

  17. Computation and Selection of Optimal Biomarker Combinations by Integrative ROC Analysis Using CombiROC

    • Mauro Bombaci, Riccardo L. Rossi
    Pages 247-259

  18. PanelomiX for the Combination of Biomarkers

    • Xavier Robin
    Pages 261-273

  19. Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework

    • Lien Nguyen, Virginie Brun, Florence Combes, Valentin Loux, Yves Vandenbrouck
    Pages 275-289

  20. Back Matter

    Pages 291-292
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Keywords

About this book

This volume presents modern and enhanced methods that detail techniques to perform proteomics analyses dedicated to biomarker discovery for human health. Chapters guide readers through pre/post analytical factors, protocols for the preparation of extracellular vesicles and exosomes, and various analytical pipelines including Data Independent Acquisition (DIA), discovery, as well as targeted and top-down proteomics analysis workflows. Bioinformatics tools and workflows to select and evaluate candidate biomarkers or combinations of biomarkers are also presented. 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 for Biomarker Discovery: Methods and Protocols aims toensure successful results in the further study of this vital field.

Editors and Affiliations

  • Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France

    Virginie Brun, Yohann Couté

Bibliographic Information

  • Book Title: Proteomics for Biomarker Discovery

  • Book Subtitle: Methods and Protocols

  • Editors: Virginie Brun, Yohann Couté

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9164-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9163-1Published: 10 March 2019

  • eBook ISBN: 978-1-4939-9164-8Published: 09 March 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 292

  • Number of Illustrations: 5 b/w illustrations, 47 illustrations in colour

  • Topics: Proteomics, Protein Science

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