ENGLISH

Proteomics for Biomarker Discovery: Methods and Protocols

By Virginie Brun , Yohann Couté

Book information

Publisher
Springer New York;Humana Press
Year
2019
ISBN
978-1-4939-9163-1, 978-1-4939-9164-8
Language
english
Format
PDF
Filesize
8 MB (8879316 bytes)
Series
Methods in Molecular Biology 1959
Edition
1st ed.
Pages
XII, 292\294
Time added
2019-04-19 19:00:00
Life Sciences; Proteomics; Protein Science

Description

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 to ensure successful results in the further study of this vital field. Front Matter ....Pages i-xii Pre- and Post-analytical Factors in Biomarker Discovery (Frank Klont, Peter Horvatovich, Natalia Govorukhina, Rainer Bischoff)....Pages 1-22 Pre-fractionation of Noncirculating Biological Fluids to Improve Discovery of Clinically Relevant Protein Biomarkers (Annarita Farina)....Pages 23-37 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 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 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 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 Lys-C/Trypsin Tandem-Digestion Protocol for Gel-Free Proteomic Analysis of Colon Biopsies (Armin Schniers, Yvonne Pasing, Terkel Hansen)....Pages 113-122 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 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 Discovering Protein Biomarkers from Clinical Peripheral Blood Mononuclear Cells Using Data-Independent Acquisition Mass Spectrometry (Xin Ku, Wei Yan)....Pages 151-161 Intact Protein Analysis by LC-MS for Characterizing Biomarkers in Cerebrospinal Fluid (Jérôme Vialaret, Sylvain Lehmann, Christophe Hirtz)....Pages 163-172 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 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 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 Protein-Level Statistical Analysis of Quantitative Label-Free Proteomics Data with ProStaR (Samuel Wieczorek, Florence Combes, Hélène Borges, Thomas Burger)....Pages 225-246 Computation and Selection of Optimal Biomarker Combinations by Integrative ROC Analysis Using CombiROC (Mauro Bombaci, Riccardo L. Rossi)....Pages 247-259 PanelomiX for the Combination of Biomarkers (Xavier Robin)....Pages 261-273 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 Back Matter ....Pages 291-292

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