Proteomic Profiling (2^nd Ed., 2nd ed. 2021)
Methods and Protocols
Methods in Molecular Biology Series, Vol. 2261

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

Includes cutting-edge techniques

Provides step-by-step detail essential for reproducible results

Contains key implementation advice from the experts