Peptidomics: Methods and Strategies

ISBN-13: 9781071636459 / Angielski

Michael Schrader; Lloyd D. Fricker

Spis treści

Part I: Foundations of Peptidomics

 

1. Origins, Technological Advancement, and Applications of Peptidomics

            Michael Schrader

 

2. Two Different Strategies for Stabilization of Brain Tissue and Extraction of Neuropeptides

            Elva Fridjonsdottir, Anna Nilsson, Lloyd D. Fricker, and Per E. Andrén

 

3. Mass Spectrometric De Novo Sequencing of Natural Peptides

            Irina D. Vasileva, Tatiana Yu. Samgina, and Albert T. Lebedev

 

4. Data-Independent Acquisition Peptidomics

            Leon Bichmann, Shubham Gupta, and Hannes Röst

 

5. Quantitative Peptidomics: General Considerations

            Lloyd D. Fricker

 

6. Quantitative Peptidomics Using Reductive Methylation of Amines

            Alexandre K. Tashima, Leandro M. de Castro, and Lloyd D. Fricker

 

7. Label-Free Quantitation of Endogenous Peptides

            Md Shadman Ridwan Abid, Haowen Qiu, and James W. Checco

 

8. Bioinformatics for Prohormone and Neuropeptide Discovery

            Bruce R. Southey, Elena V. Romanova, Sandra L. Rodriguez-Zas, and Jonathan V. Sweedler

 

9. Integrating a Multi-Label Deep Learning Approach with Protein Information to Compare Bioactive Peptides in Brain and Plasma

            Alexander G.B. Grønning and Camilla Schéele

 

Part II: Applications Using Non-Human Model Systems

 

10. Methods for Intracellular Peptidomic Analysis

            Rosangela A.S. Eichler, Luiz Felipe Martucci, Leandro M. de Castro, and Emer S. Ferro

 

11. Neuropeptidomics of Genetically Defined Cell Types in Mouse Brain

            Lloyd D. Fricker

 

12. Non-Targeted Identification of d-Amino Acid-Containing Peptides through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS

            Samuel Okyem, Elena V. Romanova, Hua-Chia Tai, James W. Checco, and Jonathan V. Sweedler

 

13. Albumen and Yolk Plasma Peptidomics for the Identification and Quantitation of Bioactive Molecules and the Quality Control of Hen Egg Products

            Simona Arena, Giovanni Renzone, Valentina Ciaravolo, and Andrea Scaloni

 

14. An Updated Guide to the Identification, Quantitation, and Imaging of the Crustacean Neuropeptidome

            Wenxin Wu, Lauren Fields, Kellen DeLaney, Amanda R. Buchberger, and Lingjun Li

 

15. Strategy for the Identification of Host-Defense Peptides in Frog Skin Secretions with Therapeutic Potential as Antidiabetic Agents

            J. Michael Conlon, R. Charlotte Moffett, Peter R. Flatt, and Jérôme Leprince

 

16. Peptidomics of Zebrafish Brain in a 6-OHDA-Induced Neurodegeneration Model

            Louise O. Fiametti, Felipe Ricardo de Mello, and Leandro M. de Castro

 

17. Analysis of the Snake Venom Peptidome

            Solange M.T. Serrano, André Zelanis, Jackson G. Miyamoto, Jackelinne Y. Hayashi, Eduardo S. Kitano, and Alexandre K. Tashima

 

18. Identification of Peptides in Spider Venom Using Mass Spectrometry

            Erika S. Nishiduka, Rafael L. Lomazi, Pedro I. da Silva Jr., and Alexandre K. Tashima

 

19. Identification and Targeted Quantification of Endogenous Neuropeptides in the Nematode Caenorhabditis elegans Using Mass Spectrometry

            Sven Van Bael, Christina Ludwig, Geert Baggerman, and Liesbet Temmerman

 

20. Intracellular and Extracellular Peptidomes of the Model Plant, Physcomitrium patens

            Irina Lyapina and Igor Fesenko

 

Part III: Clinical Applications and Outlook

 

21. The Strategy for Peptidomic LC-MS/MS Data Analysis: The Case of Urinary Peptidome Study

            Natalia V. Zakharova, Anna E. Bugrova, Maria I. Indeykina, Alexander G. Brzhozovskiy, Evgeny N. Nikolaev, and Alexey S. Kononikhin

 

22. Peptidomics Strategies to Evaluate Cancer Diagnosis, Prognosis, and Treatment

            Daniella Figueiredo, Rodrigo G.B. Cruz, Ana Gabriela Costa Normando, Daniela C. Granato, Ariane F. Busso-Lopes, Carolina M. Carnielli, Tatiane De Rossi, and Adriana Franco Paes Leme

 

23. Mass Spectrometry-Based Immunopeptidomics of Peptides Presented on Human Leukocyte Antigen Proteins

            Hesham ElAbd and Andre Franke

 

24. Profiling Human Cerebrospinal Fluid (CSF) Endogenous Peptidome in Alzheimer's Disease

            Danqing Wang, Zhengwei Chen, and Lingjun Li

 

25. Deep Learning-Assisted Analysis of Immunopeptidomics Data

            Wassim Gabriel, Mario Picciani, Matthew The, and Mathias Wilhelm

 

26. Current Challenges and Future Directions in Peptidomics

            Michael Schrader and Lloyd D. Fricker

Blurb

This updated edition explores essential techniques and newly emerged applications used in the expanding field of peptidomics. The opening chapters describe sample preparation and basic techniques. Subsequent chapters delve into quantitative peptidomics, bioinformatics, deep learning approaches, non-human model organisms, and peptide toxins. The last section includes multiple chapters on applications of peptidomics for human clinical specimens. Written for the highly successful Methods in Molecular Biology series, chapters include overviews and introductions to their respective topics, lists of the necessary materials, reagents, and instrumentation, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and up-to-date, Peptidomics: Methods and Strategies, Second Edition serves as an ideal guide for state-of-the-art approaches in this vital field.