Proteomic Profiling: Methods and Protocols

1. How Modern Mass Spectrometry Can Solve Ancient Questions: A multi-Omics Study of the Stomach Content of the Oldest Human Ice Mummy, the 5300-Year-Old Iceman or Oetzi            Rudolf Grimm 2. Step-by-Step Sample Preparation of Proteins for Mass Spectrometric Analysis            Xinping Li, Thomas Franz, Ilian Atanassov, and Thomas Colby 3. Lab-on-a-Filter Techniques for Economical, Effective, and Flexible Proteome Analysis            Yi-Han Lin, Rodrigo Vargas Eguez, Isha Vashee, and Yanbao Yu 4. Released N-Glycan Analysis for Biotherapeutic Development Using Liquid Chromatography and Mass Spectrometry            Ximo Zhang 5. Comprehensive Protocol to Simultaneously Study Protein Phosphorylation, Acetylation, and N-Linked Sialylated Glycosylation            Marcella Nunes Melo-Braga, María Ibáñez-Vea, Katarzyna Kulej, and Martin R. Larsen 6. Phos-Tag Fluorescent Gel Staining for the Quantitative Detection of His- and Asp-Phosphorylated Proteins            Emiko Kinoshita-Kikuta, Eiji Kinoshita, and Tohru Koike 7. Polyubiquitin Profile in Down Syndrome and Alzheimer Disease Brain            Antonella Tramutola and Marzia Perluigi 8. Platform Methods to Characterize the Charge Heterogeneity of Three Common Protein Therapeutics by Imaged Capillary Isoelectric Focusing            Jiaqi Wu, Will McElroy, Charles Haitjema, Carsten Lück, and Christopher Heger 9. A Protocol for Isolation, Purification, Characterization, and Functional Dissection of Exosomes            Alin Rai, Haoyun Fang, Monique Fatmous, Bethany Claridge, Qi Hui Poh, Richard J. Simpson, and David W. Greening 10. Human Plasma Extracellular Vesicle Isolation and Proteomic Characterization for the Optimization of Liquid Biopsy in Multiple Myeloma            Antonia Reale, Tiffany Khong, Rong Xu, Maoshan Chen, Sridurga Mithraprabhu, Nicholas Bingham, Andrew Spencer, and David W. Greening 11. Isolation of Extracellular Vesicles for Proteomic Profiling            Dongsic Choi, Janusz Rak, and Yong Song Gho 12. Isolation of Proteins from Extracellular Vesicles (EVs) for Mass Spectrometry-Based Proteomic Analyses            Prabal Subedi, Michael Schneider, Michael J. Atkinson, and Soile Tapio 13. Flow Cytometry as an Important Tool in Proteomic Profiling            Michael P. Blundell, Sharon L. Sanderson, and Tracey A. Long 14. Improved Immunoprecipitation to Mass Spectrometry Method for Enrichment of Low-Abundant Protein Targets            Penny Jensen, Bhavin Patel, Suzanne Smith, Renuka Sabnis, and Barbara Kaboord 15. Multiplex Fluorescent Bead-Based Immunoassay for the Detection of Cytokines, Chemokines, and Growth Factors            Jonathan M. Preuss, Ute Burret, and Sabine Vettorazzi 16. Bead-Based Multiplex Immunoassays: Procedures, Tips, and Tricks            Candice Cox 17. Immunoaffinity-Based Liquid Chromatography Mass Spectrometric Assay to Accurately Quantify the Protein Concentration of HMGB1 in EDTA Plasma            Viktoria Anselm, Andreas Steinhilber, Cornelia Sommersdorf, and Oliver Poetz 18. Recombinant Anti-Idiotypic Antibodies in Ligand Binding Assays for Antibody Drug Development            Stefan Harth and Christian Frisch 19. cDNA Display-Mediated Immuno-PCR (cD-IPCR): An Ultrasensitive Immunoassay for Biomolecular Detection            Chathuni Jayathilake and Naoto Nemoto 20. Chromatin Immunoprecipitation (ChIP) to Study DNA-Protein Interactions            Eliza C. Small, Danielle Maryanski, Kevin J. Harvey, Michael-C. Keogh, and Andrea Johnstone 21. Profiling Protein-DNA Interactions by Chromatin Immunoprecipitation in Arabidopsis            Hendry Susila, Zeeshan Nasim, Suhyun Jin, Geummin Youn, Hyewon Jeong, Ji-Yul Jung, and Ji Hoon Ahn 22. Biotin Proximity Labeling for Protein-Protein Interaction Discovery: The BioID Method            Jeff E. Habel 23. Studying OTUD6B-OTUB1 Protein-Protein Interaction by Low-Throughput GFP-Trap Assays and High-Throughput AlphaScreen Assays            Elisabeth Weber, Kenji Schorpp, and Kamyar Hadian 24. Thermal Shift Assay for Exploring Interactions between Fatty Acid-Binding Protein and Inhibitors            Jiaqing Hao 25. Isolation and Purification of Mitochondria from Cell Culture for Proteomic Analyses            Yaschar Kabiri, Christine von Toerne, Adriana Fontes, Percy A. Knolle, and Hans Zischka 26. Investigating the Adipose Tissue Secretome: A Protocol to Generate High Quality Samples Appropriate for Comprehensive Proteomic Profiling            Sonja Hartwig, Jorg Kotzka, and Stefan Lehr 27. Methods for Proteomics-Based Analysis of the Human Muscle Secretome Using an In Vitro Exercise Model            Cora Weigert, Sonja Hartwig, and Stefan Lehr 28. Western Blotting Using In-Gel Protein Labeling as a Normalization Control: Advantages of Stain-Free Technology            Rômulo Leão Silva Neris, Andrea Marie Chua Dobles, and Aldrin V. Gomes 29. Technical Considerations for Contemporary Western Blot Techniques            Kenneth Oh 30. Simple Western: Bringing the Western Blot into the 21st Century            Carsten Lück, Charles Haitjema, and Christopher Heger 31. Development of Peptide Ligands for Targeted Capture of Host Cell Proteins from Cell Culture Production Harvests            R. Ashton Lavoie, Taufika Islam Williams, R. Kevin Blackburn, Ruben G. Carbonell, and Stefano Menegatti 32. Sample Preparation of Secreted Mammalian Host Cell Proteins and their Characterization by Two-Dimensional Electrophoresis and Western Blotting            Anton Posch, Franziska Kollmann, Thomas Berkelman, and Elizabeth Dreskin 33. Quantitative Proteomic Analysis Using Formalin-Fixed Paraffin-Embedded (FFPE) Human Cardiac Tissue            Omid Azimzade1, Mike J. Atkinson, and Soile Tapio 34. Chloroplast Isolation and Enrichment of Low Abundant Proteins by Affinity Chromatography for Identification in Complex Proteomes            Roman G. Bayer, Simon Stael, and Markus Teige 35. Principles of Protein Labeling Techniques            Christian Obermaier, Anja Griebel, and Reiner Westermeier 36. Mechanical/Physical Methods of Cell Disruption and Tissue Homogenization            Stanley Goldberg... Mehr