Proteomics for Biomarker Discovery

ISBN-13: 9781493959990 / Angielski / Miękka / 2016 / 320 str.

Ming Zhou; Timothy Veenstra

Opis

With the advent of proteomics came the development of technologies, primarily mass spectrometry, which allowed high-throughput identification of proteins in complex mixtures. While the mass spectrometer resides at the heart of proteomics, its ability to characterize biological samples is only as good as the sample preparation and data analysis tools used in any study. In Proteomics for Biomarker Discovery, expert researchers in the field detail many of the methods which are now commonly used to study proteomics. These include methods and techniques include both label-free approaches and those that utilize stable isotopes incorporated both during cell growth or added via a chemical reaction once the proteome is extracted from the cell. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Proteomics for Biomarker Discovery seeks to aid scientists in the further study the different sample preparation and data analysis tools used in proteomics today.

Spis treści

 1. Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis

Julian A. J. Jaros, Paul C. Guest, Sabine Bahn, and Daniel Martins-de-Souza

2. Tissue Sample Preparation for Biomarker Discovery

Yoshiyuki Suehara,  Daisuke Kubota, and Tsuyoshi Saito

3. Subcellular Fractionation for Identification of Biomarkers: Serial Detergent Extraction by Subcellular Accessibility and Solubility

Sun-Il Hwang and David K. Han

 4. Analysis of Secreted Proteins

Valeria Severino, Annarita Farina, and Angela Chambery

 5. Preparation of Human Cerebrospinal Fluid for Proteomics Biomarker Analysis

Timothy J. Waybright

 6. Proteomic Analysis of Frozen Tissue Samples Using Laser Capture Microdissection

Sumana Mukherjee, Jaime Rodriguez-Canales, Jeffrey Hanson, Michael R. Emmert-Buck, Michael A. Tangrea, DaRue A. Prieto, Josip Blonder, Donald J. Johann Jr.

 7. Use of Formalin Fixed, Paraffin Embedded Tissue for Proteomic Biomarker Discovery

David B. Krizman and Jon Burrows

 8. Phosphopeptide Enrichment Using Offline Titanium Dioxide Columns for Phosphoproteomics

Li-Rong Yu and Timothy D. Veenstra

 9. iTRAQ-Labeling for Biomarker Discovery

Leroi V. DeSouza, Sébastien N. Voisin, and K. W. Michael Siu

 10. Analysis of Glycoproteins for Biomarker Discovery

Jintang He, Yashu Liu, Jing Wu and David M. Lubman

 11. SILAC in Biomarker Discovery

Benjamin C. Orsburn

 12. Trypsin-mediated ¹⁸O/¹⁶O Labeling for Biomarker Discovery

Xiaoying Ye, King C. Chan, DaRue A. Prieto, Brian T. Luke, Donald J. Johann Jr,

Luke H. Stockwin, Dianne L. Newton, and Josip Blonder

 13. Two-dimensional SDS-PAGE Fractionation of Biological Samples for Biomarker Discovery

Thierry Rabilloud, and Sarah Triboulet

 14. Informatics of Protein and Post-Translational Modification Detection via Shotgun Proteomics

Jerry D. Holman, Surendra Dasari, and David L. Tabb

 15. Quantitation of C-Met Tyrosine Phosphorylation Using MRM-MS

Zhaojing Meng, Apurva K. Srivastava, Ming Zhou, Timothy D. Veenstra

 16. Preparation of Human Serum for Prolactin Measurement by Multiple Reaction Monitoring Mass Spectrometry

Timothy J. Waybright, Xia Xu, Jessica M. Faupel-Badger, Zhen Xiao

 17. Label-Free Quantitative Shotgun Proteomics Using Normalized Spectral Abundance Factors

Karlie A. Neilson, Tim Keighley, Dana Pascovici, Brett Cooke, and Paul A. Haynes

 18. Employment of Complementary Dissociation Techniques for Body Fluid Characterization and Biomarker Discovery

David M. Good and Dorothea Rutishauser

 19. DPhosphopeptide Microarrays for Comparative Proteomic Profiling of Cellular Lysates

Liqian Gao, Hongyan Sun, Mahesh Uttamchandani, and Shao Q. Yao

 20. Tissue Preparation for MALDI MS Imaging of Protein and Peptides

Simona Colantonio and Roberta M. Smith

 21. Plant Proteogenomics: From Protein Extraction to Improved Gene Predictions

Brett Chapman, Natalie Castellana, Alex Apffel, Ryan Ghan, Grant R. Cramer, Matthew Bellgard, Paul A. Haynes, and Steven C. Van Sluyter

 22. Label-free Differential Analysis of Murine Postsynaptic Densities

Scott P. Goulding, Michael J. MacCoss, and Christine C. Wu

 23. Fractionation of Peptides by Strong Cation Exchange Liquid Chromatography

King C. Chan and Haleem J. Issaq

Blurb

With the advent of proteomics came the development of technologies, primarily mass spectrometry, which allowed high-throughput identification of proteins in complex mixtures.  While the mass spectrometer resides at the heart of proteomics, its ability to characterize biological samples is only as good as the sample preparation and data analysis tools used in any study.  In Proteomics for Biomarker Discovery, expert researchers in the field detail many of the methods which are now commonly used to study proteomics. These methods and techniques include both label-free approaches and those that utilize stable isotopes incorporated both during cell growth or added via a chemical reaction once the proteome is extracted from the cell. 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 key tips on troubleshooting and avoiding known pitfalls.

 

 

Authoritative and practical, Proteomics for Biomarker Discovery seeks to aid scientists in the further study of the different sample preparation and data analysis tools used in proteomics today.