Proteomics for Biomarker Discovery

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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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.

• Discovery proteomics analysis
• Biomarker candidates
• Precision medicine
• LC-MS/MS analysis
• Data science
• Pathogenic mechanisms
• Proteomics

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

  Virginie Brun, Yohann Couté

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