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Clinical Proteomics

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Fernando J. Corrales

    1. Proteomics Unit, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

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  2. Alberto Paradela

    1. Proteomics Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain

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    You can also search for this editor in PubMed   Google Scholar

  3. Miguel Marcilla

    1. Proteomics Unit, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

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    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 key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2420)

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About this book

This detailed volume explores techniques in clinical proteomics, an emerging discipline aimed at deciphering the molecular mechanisms underlying the progression of diseases and at identifying new biomarkers and therapeutic targets to expand the physicians’ toolbox for precision medicine-based patient care. From sample processing to multi-omics approaches, the book provides straight-forward protocols on a wide array of vital areas of study. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Clinical Proteomics: Methods and Protocols serves as an ideal guide for researchers working to expand upon the knowledge base needed to push forward toward a more personalized version of medicine.

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Bile Processing Protocol for Improved Proteomic Analysis

    • Sergio Ciordia, Gloria Alvarez-Sola, María Rullán, Jesús M. Urman, Matías A. Ávila, Fernando J. Corrales
    Pages 1-10

  3. MS-Based Extracellular Vesicle (EVs) Analysis: An Application to Helminth-Secreted EVs

    • Javier Sotillo
    Pages 11-20

  4. Proteomic Profiling of Cerebrospinal Fluid by 16-Plex TMT-Based Mass Spectrometry

    • Kaushik Kumar Dey, Huan Sun, Zhen Wang, Mingming Niu, Hong Wang, Yun Jiao et al.
    Pages 21-37

  5. Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation

    • Daisuke Nakajima, Osamu Ohara, Yusuke Kawashima
    Pages 39-52

  6. Sample Processing for Metaproteomic Analysis of Human Gut Microbiota

    • Carmen García-Durán, Raquel Martínez-López, Lucía Monteoliva, Concha Gil
    Pages 53-61

  7. Mass Spectrometry-Based Analytical Strategy for Single-Cell Proteomics

    • Ákos Végvári
    Pages 63-72

  8. Lysine Acetylation Stoichiometry Analysis at the Proteome Level

    • Jeovanis Gil, Sergio Encarnación-Guevara
    Pages 73-86

  9. Implementation of Clinical Phosphoproteomics and Proteomics for Personalized Medicine

    • Pedro Casado, Maruan Hijazi, Henry Gerdes, Pedro R. Cutillas
    Pages 87-106

  10. pH/Acetonitrile-Gradient Reversed-Phase Fractionation of Enriched Hyper-Citrullinated Library in Combination with LC–MS/MS Analysis for Confident Identification of Citrullinated Peptides

    • Aneta Stachowicz, Niveda Sundararaman, Vidya Venkatraman, Jennifer Van Eyk, Justyna Fert-Bober
    Pages 107-126

  11. Purification of HLA Immunopeptidomes from Human Thymus

    • Iñaki Alvarez
    Pages 127-136

  12. Generation of HLA Allele-Specific Spectral Libraries to Identify and Quantify Immunopeptidomes by SWATH/DIA-MS

    • Kevin Kovalchik, David Hamelin, Etienne Caron
    Pages 137-147

  13. Immunopeptidomic Analysis of the Phosphopeptidome Displayed by HLA Class I Molecules

    • Miguel Marcilla
    Pages 149-158

  14. Development of a Standardized MRM Method for the Quantification of One Carbon Metabolism Enzymes

    • Laura Guerrero, Alberto Paradela, Fernando J. Corrales
    Pages 159-175

  15. Molecular Histology Analysis of Cryopreserved Tissue Using Peptide/Protein MALDI-TOF Imaging Mass Spectrometry (MALDI-IMS)

    • Ibon Iloro, Iraide Escobés, Mikel Azkargorta, Félix Elortza
    Pages 177-190

  16. The Human Protein Atlas and Antibody-Based Tissue Profiling in Clinical Proteomics

    • Borbala Katona, Cecilia Lindskog
    Pages 191-206

  17. Microbial Identification in the Clinical Microbiology Laboratory Using MALDI-TOF-MS

    • Iván Bloise, M. Teresa Corcuera, Julio García-Rodríguez, Jesús Mingorance
    Pages 207-216

  18. Combining Electron Microscopy (EM) and Cross-Linking Mass Spectrometry (XL-MS) for Structural Characterization of Protein Complexes

    • Lucía Quintana-Gallardo, Moisés Maestro-López, Jaime Martín-Benito, Miguel Marcilla, Daniel Rutz, Johannes Buchner et al.
    Pages 217-232

  19. Accurate Prediction of Protein Sequences for Proteogenomics Data Integration

    • Yanick Paco Hagemeijer, Victor Guryev, Peter Horvatovich
    Pages 233-260

  20. Back Matter

    Pages 261-264
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Editors and Affiliations

  • Proteomics Unit, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

    Fernando J. Corrales, Miguel Marcilla

  • Proteomics Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain

    Alberto Paradela

Bibliographic Information

  • Book Title: Clinical Proteomics

  • Book Subtitle: Methods and Protocols

  • Editors: Fernando J. Corrales, Alberto Paradela, Miguel Marcilla

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1936-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-1935-3Published: 15 December 2021

  • Softcover ISBN: 978-1-0716-1938-4Published: 16 December 2022

  • eBook ISBN: 978-1-0716-1936-0Published: 14 December 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 264

  • Number of Illustrations: 3 b/w illustrations, 39 illustrations in colour

  • Topics: Chemistry/Food Science, general, Medicine/Public Health, general

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