Main description:

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.

Contents:

1. Bile Processing Protocol for Improved Proteomic Analysis

Sergio Ciordia, Gloria Alvarez-Sola, Maria Rullan, Jesus M. Urman, Matias A. Avila, and Fernando J. Corrales

2. MS-Based Extracellular Vesicles (EVs) Analysis: An Application to Helminth-Secreted EVs

Javier Sotillo

3. 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, Xiaojun Sun, Yuxin Li, and Junmin Peng

4. 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, and Yusuke Kawashima

5. Sample Processing for Metaproteomic Analysis of Human Gut Microbiota

Carmen Garcia-Duran, Raquel Martinez Lopez, Lucia Monteoliva, and Concha Gil

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

Akos Vegvari

7. Lysine Acetylation Stoichiometry Analysis at the Proteome Level

Jeovanis Gil and Sergio Encarnacion-Guevara

8. Implementation of Clinical Phosphoproteomics and Proteomics for Personalized Medicine

Pedro Casado, Maruan Hijazi, Henry Gerdes, and Pedro R. Cutillas

9. 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, and Justyna Fert-Bober

10. Purification of HLA Immunopeptidomes from Human Thymus

Inaki Alvarez

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

David Hamelin, Etienne Caron, and Kevin Kovalchik

12. Immunopeptidomic Analysis of the Phosphopeptidome Displayed by Hla Class I Molecules

Miguel Marcilla

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

Laura Guerrero, Alberto Paradela, and Fernando J. Corrales

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

Ibon Iloro, Iraide Escobes, Mikel Azkargorta, and Felix Elortza

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

Borbala Katona and Cecilia Lindskog

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

Ivan Bloise, M. Teresa Corcuera, Julio Garcia-Rodriguez, and Jesus Mingorance

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

Lucia Quintana-Gallardo, Moises Maestro-Lopez, Jaime Martin-Benito, Miguel Marcilla, Daniel Rutz, Johannes Buchner, Jose M. Valpuesta, and Jorge Cuellar

18. Accurate Prediction of Protein Sequences for Proteogenomics Data Integration

Yanick Paco Hagemeijer, Victor Guryev, and Peter Horvatovich