Table of Contents

1. Crosstalk between cellular metabolism and histone acetylation
Sophie Trefely, Mary T. Doan and Nathaniel W. Snyder
2. Purification and enzymatic assay of class I histone deacetylase enzymes
Mark K. Adams, Charles A.S. Banks, Sayem Miah, Maxime Killer and Michael P. Washburn
3. Multiplexed quantitative phosphoproteomics of cell line and tissue samples
Johannes Kreuzer, Amanda Edwards and Wilhelm Haas
4. Differentiation of peptide isomers and epimers by radical-directed dissociation
Tyler R. Lambeth and Ryan R. Julian
5. Biochemical analysis of protein arginylation
Junling Wang, John R. Yates and Anna Kashina
6. Site-specific determination of lysine acetylation stoichiometries on the proteome-scale
Yue Chen and Yunan Li
7. RNA modifications and the link to human disease
Amber Yanas and Kathy Fange Liu
8. Isolation and characterization of glycosylated neuropeptides
Yang Liu, Qinjingwen Cao and Lingjun Li
9. Utilizing intein trans-splicing for in vivo generation of site-specifically modified proteins
Igor Maksimovic, Devin Ray, Qingfei Zheng and Yael David
10. Systematic and site-specific analysis of N-glycoproteins on the cell surface by integrating bioorthogonal chemistry and MS-based proteomics
Fangxu Sun and Ronghu Wu
11. Silencing glycosaminoglycan functions in mouse embryonic stem cells with small molecule antagonists
Sourav Chatterjee, Tesia N. Stephenson, Austen L. Michalak, Kamil Godula and Mia L. Huang
12. Biochemical and structural analysis of N-terminal acetyltransferases
Leah Gottlieb and Ronen Marmorstein
13. Site-specific analysis of the Asp- and Glu-ADP-ribosylated proteome by quantitative mass spectrometry
Peng Li, Yuanli Zhen and Yonghao Yu
14. Analysis of the topology of ubiquitin chains
Lucia Geis-Asteggiante, Amanda E. Lee and Catherine Fenselau
15. Analysis of cardiac troponin proteoforms by top-down mass spectrometry
Timothy N. Tiambeng, Trisha Tucholski, Zhijie Wu, Yanlong Zhu, Stanford D. Mitchell, David S. Roberts, Yutong Jin and Ying Ge
16. Assays for tyrosine phosphorylation in human cells
Monica Kruk, Naomi Widstrom, Sampreeti Jena, Nicole L. Wolter, John F. Blankenhorn, Ibrahim Abdalla, Tzu-Yi Yang and Laurie L. Parker
17. Metabolomics analysis of lipid metabolizing enzyme activity
Timothy B. Ware, Myungsun Shin and Ku-Lung Hsu
18. Simplified high yield TAILS terminomics using a new HPG-ALD 800K-2000 polymer with precipitation
Nestor Solis, Anilkumar Parambath, Srinivas Abbina, Jayachandran Kizhakkedathu and Christopher M. Overall
19. Methods for the expression, purification, and crystallization of histone deacetylase 6–inhibitor complexes
Jeremy D. Osko and David W. Christianson
20. Quantitative analysis of global protein lysine methylation by mass spectrometry
Peder J. Lund, Stephanie M. Lehman and Benjamin A. Garcia
21. The roles of S-nitrosylation and S-glutathionylation in Alzheimer’s disease
Ryan R. Dyer, Katarena I. Ford and Renã A. S. Robinson
22. Expression of authentic post-translationally modified proteins in organisms with expanded genetic codes
Kyle Mohler and Jesse Rinehart
23. Preparation of a new construct of human histone deacetylase 8 for the crystallization of enzyme-inhibitor complexes
Nicholas J. Porter and David W. Christianson
24. Methods for characterizing protein acetylation during viral infection
Laura A. Murray, Ashton N. Combs, Pranav Rekapalli and Ileana M. Cristea

About the Author

Benjamin A. Garcia, Ph.D., Presidential Professor, Professor of Biochemistry and Biophysics, Director of Quantitative Proteomics, Penn Epigenetics Institute, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, University of Pennsylvania School of Medicine