Proteomics for Biomarker Discovery: Methods and Protocols

1. Pre- and Post-Analytical Factors in Biomarker Discovery

            Frank Klont, Peter Horvatovich, Natalia Govorukhina, and Rainer Bischoff

2. Pre-Fractionation of Non-Circulating Biological Fluids to Improve Discovery of Clinically Relevant Protein Biomarkers

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

            Rosana Navajas, Fernando J. Corrales, and Alberto Paradela

4. Protein Biomarker Discovery Using Human Blood Plasma Microparticles

            Raghda Saad Zaghloul Taleb, Pacint Moez, Doreen Younan, Martin Eisenacher, Matthias Tenbusch, Barbara Sitek, and Thilo Bracht

5. 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, and Gregg B. Morin

6. 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, and Loïc Dayon

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

            Armin Schniers, Yvonne Pasing, and Terkel Hansen

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

            Leslie Muller, Luc Fornecker, Sarah Cianferani, and Christine Carapito

9. 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, and Anne-Marie Hesse

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

            Xin Ku and Wei Yan

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

            Jérôme Vialaret, Sylvain Lehmann, and Christophe Hirtz

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

            Didia Coelho Graça, Ralf Hartmer, Wolfgang Jabs, Alexander Scherl, Lorella Clerici, Kaveh Samii, Yury O. Tsybin, Denis Hochstrasser, and Pierre Lescuyer

13. 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, and Axel Ducret

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

            Georgia Kontostathi, Manousos Makridakis, Vasiliki Bitsika, Nikolaos Tsolakos, Antonia Vlahou, and Jerome Zoidakis

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

            Samuel Wieczorek, Florence Combes, Hélène Borges, and Thomas Burger

16. Computation and Selection of Optimal Biomarker Combinations by Integrative ROC Analysis using CombiROC

            Mauro Bombaci and Riccardo L. Rossi

17. PanelomiX for the Combination of Biomarkers

            Xavier Robin

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

            Lien Nguyen, Virginie Brun, Florence Combes, Valentin Loux, and Yves Vandenbrouck