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This book details up-to-date and cutting edge compilation of protocols in mass cytometry. Chapters guide readers through setting up a facility, panel design and reagent preparation, sample preparation, specific applications, and data analysis. 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 cutting-edge, Mass Cytometry: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Mass Cytometry: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

Part I Setting Up a Facility

1. Setting up Mass Cytometry in a Shared Resource Lab Environment
Sarah Warth and Désirée Kunkel

2. Acquisition, Processing, and Quality Control of Mass Cytometry Data
Brian H. Lee and Adeeb H. Rahman

Part II Panel Design and Reagent Preparation

3. Visualization of Mass Cytometry Signal Background to Enable Optimal Core Panel Customization and Signal Threshold Gating 
Amelia Au-Yeung, Chikara Takahashi, William Mathews, and William E. O'Gorman

4. Method for Tagging Antibodies with Metals for Mass Cytometry Experiments
Stephen Gregory Chang and Cynthia J. Guidos

5. Scalable Conjugation and Characterization of Immunoglobulins with Stable Mass Isotope Reporters for Single-Cell Mass Cytometry Analysis
Felix J. Hartmann, Erin F. Simonds, Nora Vivanco, Trevor Bruce, Luciene Borges, Garry P. Nolan, Matthew H. Spitzer, and Sean C. Bendall

6. Titration of Mass Cytometry Reagents
Caryn van Vreden, Paula Niewold, Helen M. McGuire, and Barbara Fazekas de St Groth

7. Cell-Surface Barcoding of Live PBMC for Multiplexed Mass Cytometry
Axel Ronald Schulz and Henrik E. Mei

Part III Sample Preparation

8. Automated Cell Processing for Mass Cytometry Experiments
Jaromir Mikes, Axel Olin, Tadepally Lakshmikanth, Yang Chen, and Petter Brodin

9. Live Cell Barcoding for Efficient Analysis of Small Samples by Mass Cytometry
Lisa E. Wagar

Part IV Specific Applications

10. Staining of Phosphorylated Signalling Markers Protocol for Mass Cytometry
Diana Shinko, Thomas Ashhurst, Helen M. McGuire, and Kellie A. Charles

11. Multiplex MHC Class I Tetramer Combined with Intranuclear Staining by Mass Cytometry
Yannick Simoni, Michael Fehlings, and Evan W. Newell

12. Analysis of the Murine Bone Marrow Haematopoietic System Using Mass and Flow Cytometry
Thomas M. Ashhurst, Darren A. Cox, Adrian L. Smith, and Nicholas J.C. King

13. Mass Cytometric Cell Cycle Analysis
Gregory K. Behbehani

14. Picturing Polarized Myeloid Phagocytes and Regulatory Cells by Mass Cytometry
Mikael Roussel, Todd Bartkowiak, and Jonathan M. Irish

15. Quantitative Measurement of Cell-nanoparticle Interactions Using Mass Cytometry
Andrew J. Mitchell, Angela Ivask, and Yi Ju

Part V Data Analysis

16. Data-Driven Flow Cytometry Analysis 
Sherrie Wang and Ryan R. Brinkman

17. Analysis of Mass Cytometry Data
Christina B. Pedersen and Lars R. Olsen

18. Analysis of High Dimensional Phenotype Data Generated by Mass Cytometry or High Dimensional Flow Cytometry
Branko Cirovic, Natalie Katzmarski, and Andreas Schlitzer

19. Computational Analysis of High Dimensional Mass Cytometry Data from Clinical Tissue Samples
Sam Norton and Roslyn Kemp

20. Supervised Machine Learning with CITRUS for Single Cell Biomarker Discovery
Hannah G. Polikowsky and Katherine A. Drake