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The use of proteomics to study complex diseases such as cardiovascular disease, the leading cause of death in developed countries, has grown exponentially in recent years. Proteomics is a rapidly expanding investigation platform in cardiovascular medicine and is becoming integrated and incorporated into cardiovascular research. The proteomics field continues to develop with major improvements in mass spectrometry instrumentation, methodology and data analysis. Heart Proteomics: Methods and Protocols complies a selection of techniques and methods that target the numerous processes implicated in the pathophysiology of heart. Chapters cover protocols and updated methods in the heart proteomic area with a particular focus on MS-based methods of protein and peptide quantification and the analysis of posttranslational modifications as well as descriptions of system biology approaches, which provide a better understanding of normal and pathological processes. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, Heart Proteomics: Methods and Protocols is a representative selection of methods that will prove to be a useful resource for experienced proteomics practitioners and newcomers alike.

Heart Proteomics: Methods and Protocols

1. Large-Scale Characterization of the Murine Cardiac Proteome

Jake Cosme, Andrew Emili, and Anthony O. Gramolini

2. Determining Protein Concentrations of the Human Ventricular Proteome

Arjen Scholten and Albert J.R. Heck

3. Multidimensional Protein Identification Technology for Direct-Tissue Proteomics of Heart

Dario Di Silvestre, Francesca Brambilla, and Pier Luigi Mauri

4. Global Protein Quantification of Mouse Heart Tissue Based on the SILAC Mouse

Anne Konzer, Aaron Ruhs, Thomas Braun, and Marcus Krüger

5. Global Proteomic Profiling and Enrichment Maps of Dilated Cardiomyopathy

Ruth Isserlin, Daniele Merico, and Andrew Emili

6. Characterization of the Human Myocardial Proteome in Dilated Cardiomyopathy by Label-Free Quantitative Shotgun Proteomics of Heart Biopsies

Elke Hammer, Katrin Darm, and Uwe Völker

7. Systems Proteomics of Healthy and Diseased Chromatin

Haodong Chen, Emma Monte, Thomas M. Vondriska, and Sarah Franklin

8. Proteomic Analysis of Interstitial Aortic Valve Cells Acquiring a Pro-Calcific Profile

Millioni Renato, Elisa Bertacco, Cinzia Franchin, Giorgio Arrigoni, and Marcello Rattazzi

9. Differential Protein Expression Analysis of Degenerative Aortic Stenosis by Itraq Labeling

Sergio Alonso-Orgaz, Tatiana Martin-Rojas, Enrique Calvo, Juan Antonio López, Fernando Vivanco, and Maria G. Barderas

10. Characterization of Zebrafish Cardiac Proteome Using On Line PH Gradient SCX -RP HPLC MS/MS Platform

Jiang Zhang, Kevin A. Lanham, Warren Heideman, Richard E. Peterson, and Lingjun Li

11. Proteomic Analysis of Brain Mitochondrial Proteome and Mitochondrial Complexes

Ana Lopez-Campistrous and Carlos Fernandez-Patron

12. Oxidative Modifications of Mitochondria Complex II

Liwen Zhang, Patrick T. Kang, Chwen-Lih Chen, Kari B. Green-Church, and Yeong-Renn Chen

13. Detection of O-GLCNAC Modifications on Cardiac Myofilament Proteins

Genaro A. Ramirez-Correa, Isabel Martinez Ferrando, Gerald Hart, and Anne Murphy

14. Quantification of Mitochondrial S-Nitrosylation by CYSTMT6 Switch Assay

Christopher I. Murray, Hea Seung Chung, Helge Uhrigshardt, and Jennifer E. Van Eyk

15. Identification of Thioredoxin Target Protein Networks in Cardiac Tissues of a Transgenic Mouse

Cexiong Fu, Tong Liu, Andrew M. Parrott, and Hong Li

16. Using Pure Protein to Build a Multiple Reaction Monitoring Mass Spectrometry Assay for Targeted Detection and Quantitation

Eric Grote, Qin Fu, Weihua Ji, Xiaoqian Liu, and Jennifer E. Van Eyk

17. A Sequential Extraction Methodology for Cardiac Extracellular Matrix Prior to Proteomics Analysis

Javier Barallobre-Barreiro, Athanasios Didangelos, Xiaoke Yin, Nieves Doménech, and Manuel Mayr

18. Optimized Method for Identification of the Proteomes Secreted by Cardiac Cells

Miroslava Stastna and Jennifer E. Van Eyk

19. Secretome of Human Aortic Valves

Fernando de la Cuesta, Gloria Alvarez-Llamas, Felix Gil-Dones, Veronica M. Darde, Enrique Calvo, Juan Antonio Lopez, Fernando Vivanco, and Maria G. Barderas

20. A Comparative Study of Immunodepletion and Equalization Methods for Aortic Stenosis Human Plasma

Felix Gil Dones, Verónica M. Darde, Fernando Vivanco, and María G. Barderas

15. Identification of Thioredoxin Target Protein Networks in Cardiac Tissues of a Transgenic Mouse

Cexiong Fu, Tong Liu, Andrew M. Parrott, and Hong Li

16. Using Pure Protein to Build a Multiple Reaction Monitoring Mass Spectrometry Assay for Targeted Detection and Quantitation

Eric Grote, Qin Fu, Weihua Ji, Xiaoqian Liu, and Jennifer E. Van Eyk

17. A Sequential Extraction Methodology for Cardiac Extracellular Matrix Prior to Proteomics Analysis

Javier Barallobre-Barreiro, Athanasios Didangelos, Xiaoke Yin, Nieves Doménech, and Manuel Mayr

18. Optimized Method for Identification of the Proteomes Secreted by Cardiac Cells

Miroslava Stastna and Jennifer E. Van Eyk

19. Secretome of Human Aortic Valves

Fernando de la Cuesta, Gloria Alvarez-Llamas, Felix Gil-Dones, Veronica M. Darde, Enrique Calvo, Juan Antonio Lopez, Fernando Vivanco, and Maria G. Barderas

20. A Comparative Study of Immunodepletion and Equalization Methods for Aortic Stenosis Human Plasma

Felix Gil Dones, Verónica M. Darde, Fernando Vivanco, and María G. Barderas

15. Identification of Thioredoxin Target Protein Networks in Cardiac Tissues of a Transgenic Mouse

Cexiong Fu, Tong Liu, Andrew M. Parrott, and Hong Li

16. Using Pure Protein to Build a Multiple Reaction Monitoring Mass Spectrometry Assay for Targeted Detection and Quantitation

Eric Grote, Qin Fu, Weihua Ji, Xiaoqian Liu, and Jennifer E. Van Eyk

17. A Sequential Extraction Methodology for Cardiac Extracellular Matrix Prior to Proteomics Analysis

Javier Barallobre-Barreiro, Athanasios Didangelos, Xiaoke Yin, Nieves Doménech, and Manuel Mayr

18. Optimized Method for Identification of the Proteomes Secreted by Cardiac Cells

Miroslava Stastna and Jennifer E. Van Eyk

19. Secretome of Human Aortic Valves

Fernando de la Cuesta, Gloria Alvarez-Llamas, Felix Gil-Dones, Veronica M. Darde, Enrique Calvo, Juan Antonio Lopez, Fernando Vivanco, and Maria G. Barderas

20. A Comparative Study of Immunodepletion and Equalization Methods for Aortic Stenosis Human Plasma

Felix Gil Dones, Verónica M. Darde, Fernando Vivanco, and María G. Barderas