Serum/Plasma Proteomics: Methods and Protocols

ISBN-13: 9781493983803 / Angielski / Miękka / 2018 / 551 str.

David W. Greening; Richard J. Simpson

Spis treści

Part I Updated Blood Processing and Handling Strategies

1. Direct Assessment of Plasma/Serum Sample Quality for Proteomics Biomarker Investigation

Viviana Greco, Cristian Piras, Luisa Pieroni, and Andrea Urbani

 

2. A Protocol for the Preparation of Cryoprecipitate and Cryo-Depleted Plasma

Rosemary L Sparrow, David W Greening, and Richard J Simpson

 

3. A Proteomic Protocol for the Preparation of Platelet Concentrates

David W Greening, Richard J Simpson, and Rosemary L Sparrow

 

Part II Updated Fractionation Strategies for In-depth Blood Proteome Analysis

4. Bead-based and Multiplexed Immunoassays for Protein Profiling via Sequential Affinity Capture

Elin Birgersson, Jochen M. Schwenk, and Burcu Ayoglu

 

5. Affinity Proteomics for Fast, Sensitive, Quantitative Analysis of Proteins in Plasma

John P O’Grady, Kevin W Meyer, and  Derrick N Poe

 

6. Characterization of the Low-molecular Weight Human Plasma Peptidome

David W. Greening and Richard J. Simpson

 

7. In-depth, Reproducible Analysis of Human Plasma using IgY 14 and SuperMix Immunodepletion

Lynn A. Beer, Bonnie Ky, Kurt T. Barnhart, and David W. Speicher

 

8. Low-Molecular-Weight Plasma Proteome Analysis Using Top-Down Mass Spectrometry

Dong Huey Cheon, Eun Gyeong Yang, Cheolju Lee, and Ji Eun Lee

 

9. Identification of Post-Translational Modifications from Serum/Plasma by Immunoaffinity Enrichment and LC-MS/MS Analysis without Depletion of Abundant Proteins

Hongbo Gu, Jianmin Ren, Xiaoying Jia, and Matthew P. Stokes

 

10. Identification of Core-fucosylated Glycoproteome in Human Plasma

Qichen Cao, Qing Zhao, Xiaohong Qian, and Wantao Ying

 

Part III Updated Proteome Analysis of Blood Cell Components, Vesicles, and Blood-related Fluids<

11. Proteomic Analysis of Blood Extracellular Vesicles in Cardiovascular Disease by LC-MS/MS Analysis

Montserrat Baldan-Martin, Fernando de la Cuesta, Gloria Alvarez-Llamas, Gema Ruiz-Hurtado, Luis M. Ruilope, and Maria G. Barderas

 

12. Targeted Approach For Proteomic Analysis of a Hidden Membrane Protein

Tania Martins-Marques, Sandra I. Anjo, Teresa Ribeiro-Rodrigues, Bruno Manadas, and Henrique Girao

 

13. Red Blood Cells in Clinical Proteomics

Ana Sofia Carvalho, Manuel S Rodriguez, and Rune Matthiesen

 

14. High-throughput Quantitative Lipidomics Analysis of Non-esterified Fatty Acids in Plasma by LC-MS

Nicolas Christinat, Delphine Morin-Rivron, and Mojgan Masoodi

 

15. Simultaneous Enrichment of Plasma Extracellular Vesicles and Glycoproteome for Studying Disease Biomarkers

Sunil S. Adav and Siu Kwan Sze

 

16. Lipidomics of Human Blood Plasma by High Resolution Shotgun Mass Spectrometry

Susanne Sales, Oskar Knittelfelder, and Andrej Shevchenko

 

17. Proteomics Analysis of Circulating Serum Exosomes

Antonius Koller, Purvi Patel, Jenny Kim Kim, and Emily I. Chen

 

Part IV Antibody-based Discovery and Targeted Proteomics

18. High-density Serum/Plasma Reverse Phase Protein Arrays

Cecilia Hellström, Tea Dodig-Crnković, Mun-Gwan Hong, Jochen M. Schwenk, Peter Nilsson, and Ronald Sjöberg

 

19. Antibody Colocalization Microarray for Cross-reactivity free Multiplexed Protein Analysis

Véronique Laforte, Pik-Shan Lo, Huiyan Li, and David Juncker

 

20. Surface Profiling of Extracellular Vesicles From Plasma or Ascites Fluid using Dotscan Antibody Microarrays

Larissa Belov, Susannah Hallal, Kieran Matic, Jerry Zhou, Sandra Wissmueller, Nuzhat Ahmed, Sumaiya Tanjil, Stephen P. Mulligan, O. Giles Best, Richard J. Simpson, and Richard I. Christopherson

 

21. Serum Profiling for Identification of Autoantibody Signatures in Diseases using Protein Microarrays

Shabarni Gupta, Manubhai K.P., Shuvolina Mukherjee, and Sanjeeva Srivastava

 

Part V Developments in Discovery and Targeted Proteomics

22. Quantitative Comparisons of Large Numbers of Human Plasma Samples using TMT10plex Labelling

Pengyuan Liu, Lynn A. Beer, Bonnie Ky, Kurt T. Barnhart, and David W. Speicher

 

23. Efficient Quantitative Comparisons of Plasma Proteomes using Label-free Analysis with MaxQuant

Lynn A. Beer, Pengyuan Liu, Bonnie Ky, Kurt T. Barnhart, and David W. Speicher

 

24. Blood and Plasma Proteomics: Targeted Quantitation and Post-translational Redox Modifications

Julie A. Reisz, Katelyn M. Chessler, Monika Dzieciatkowska, Angelo D’Alessandro, and Kirk C. Hansen

 

25. SWATH Mass Spectrometry for Proteomics of Non-depleted Plasma

Christoph Krisp and Mark P. Molloy 

26. Shotgun and Targeted Plasma Proteomics to Predict Prognosis of Non-Small Cell Lung Cancer

Qing-Run Li, Yan-Sheng Liu, and Rong Zeng

 

27. High-throughput Parallel Proteomic Sample Preparation using 96-well Polyvinylidene Fluoride (PVDF) Membranes and C18 Purification Plates

Tue Bjerg Bennike and Hanno Steen

 

28. Targeted Quantification of the Glycated Peptides of Human Serum Albumin

Garikapati Vannuruswamy, Arvind M Korwar, Mashanipalya G Jagadeeshaprasad, and Mahesh J Kulkarni

 

29. Absolute Quantification of Middle to High Abundant Plasma Proteins via Targeted Proteomics

Julia Dittrich and Uta Ceglarek

 

Part VI. Developments in Biomarker Discovery

30. A Highly Automated Shotgun Proteomic Workflow – Clinical Scale and Robustness for Biomarker Discovery in Blood

Loïc Dayon, Antonio Núñez Galindo, Ornella Cominetti, John Corthésy, and Martin Kussmann

 

31. Mass Spectrometry-based Serum Proteomics for Biomarker Discovery and Validation

Santosh D. Bhosale, Robert Moulder, Petri Kouvonen, Riitta Lahesmaa, and David R. Goodlett

 

32. Metabolomics Towards Biomarker Discovery

Peiyuan Yin and Guowang Xu

 

33. Plasma Biomarker Identification and Quantification by Microparticle Proteomics

Michal Harel and Tamar Geiger

 

34. Bronchoalveolar Lavage Quantitative Mass Spectrometry based Proteomics Analysis in Lung Diseases

Ana Sofia Carvalho and Rune Matthiesen

 

35. Protein Multiplexed Immunoassay Analysis with R

Edmond J Breen

 

Appendix

Blurb

Over the past decade, there has been an increase in powerful proteomics technologies that allow greater fundamental insights into the blood proteome. Further developments in informatic analyses, software developments, and computational tools are providing insights into large data sets, open-source data along with large-scale application of bioinformatics. Serum/Plasma Proteomics: Methods and Protocols, Second Edition is a comprehensive resource of protocols for areas, pre-analytical through to analytical, of plasma and serum proteomics. Divided into five convenient sections, covering fractionation strategies for in-depth blood proteome analysis, defined procedures for blood collection, handling and storage, detailed protocols for performing both antibody-based and non-antibody based quantitative assays,  proteome analysis of blood cell compartments, circulating nanomebraneous vesicles and blood-related fluids, data management, statistical design, and bioinformatic challenges. 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 practical, Serum/Plasma Proteomics: Methods and Protocols, Second Edition delivers a valuable foundation for the development and application of blood-based proteomics, and further incorporates blood cell components, including platelets, red blood cells, circulating extracellular vesicles/exosomes, and related biofluids.