Note: Intro -- RECENT ADVANCES IN PROTEOMICS RESEARCH -- Library of Congress Cataloging-in-Publication Data -- Contents -- Preface -- Chapter 1 Protein Level Analysis from Specific Cell Types in Heterogeneous Tissue -- Abstract -- Introduction -- Laser Capture Microdissection and the Proteome -- Immuno-LCM -- Immuno-PCR -- Biobarcoding and Nanoparticles -- Aptamers -- Mass Spectrometry -- Discussion -- Acknowledgments -- References -- Chapter 2 Neuroproteomics and Its Applicationin Drug Addiction Study -- Abstract -- 1. Introduction -- 2. Proteome Dynamics and Complexity in Substance Abuse Research -- 3. Proteomic Techniques -- 4. Bioinformatics -- 5. Challenges and Limitations of Neuroproteomics Approaches -- 6. Protein arrays -- 7. Recent Applications of Neuroproteomics in Research on Nicotine and Other Substances of Abuse -- 8. Proteomics Provides Insights into Mechanisms Underlying Drug Addiction -- Summary and Conclusion -- Acknowledgments -- References -- Chapter 3 Current Proteomics Methods for Analysing the Human Microbiome -- Abstract -- Introduction -- Proteomics in Bacterial Research -- Proteomic Tools -- Protein Identification -- The Limits of Proteomics -- Future Directions -- References -- Chapter 4 Analysis of Pleural Fluid: The Path Travelled with Proteomic Guidance -- Abstract -- 1. Introduction -- 2. Why Proteomics? - Limitations of Microscopic Analysis of Pleural Fluid -- 3. Pre-Analytic and Intra-Analytical Variables of the Pleural Fluid Proteome -- 4. The Pleural Fluid Proteome is a Great Place to Search for Cancer Biomarkers - Why? -- 5. Early Efforts - Challenges and Promising Discoveries -- 6. Cancer Specific Discovery Proteomic Efforts -A Gold Mine of Information -- 7. Secretome Analysis with Pleural Effusion Proteome Study - A Promising Path -- 8. Recent Studies with Mudpit and Other Methods- Many New Biomarker Candidates. , Conclusion -- References -- Chapter 5 Application of Quantitative Proteomics to Disease Diagnosis and Prognosis Using Stable Isotope Dimethyl Labeling Coupled with Shotgun Proteomics Strategy and Multiple Reaction Monitoring -- Abstract -- 1. Introduction -- 2. Proteomic Methodologies and Platforms -- 3. Proteomics Study on Three Exemplar Clinical Cases -- Conclusion -- Acknowledgments -- References -- Chapter 6 Mitochondria Protein Profilingin Striated Muscle: Insights into Pathophysiological Conditions -- Abstract -- 1. Introduction -- 2. Mitochondrial Proteome Characterization in Striated Muscle -- 3. Mitochondrial Proteome Plasticity in Pathophysiological Conditions -- 4. Future Perspectives -- Acknowledgments -- References -- Chapter 7 Structural Mass Spectrometry of Halophilic Proteasomal Nanomachines Using Chemical Cross-Linking -- Abstract -- Introduction -- Structural Mass Spectrometry -- General Principle and Strategies of CXMS -- Characteristics of Cross-Linkers -- Bioinformatics in Cross-Link Identification -- CXMS and Comparative Modeling -- Investigation of Multiprotein Complexes by Methods of Structural Proteomics -- Software to Incorporate CXMS Distance Constraints for Validation of Theoretical Models -- Case Study: The Multiprotein 20S Proteasome Core Particles of Haloarchaea -- Specificity of Halophilic Haloarchaeal CP Nanomachines and Strategy of Its Investigation -- Use of Cross-Linking Distance Constraints to Optimize Models of Halophilic Multisubunit Complexes on a Routine Basis -- Conclusion -- Acknowledgments -- References -- Chapter 8 Introduction to Protein Arrays and their Application to Nicotine Research in Macrophages -- Abstract -- Introduction -- Designs of Protein Arrays -- Array Data Processing and Analysis -- Application of Protein Arrays to Nicotine Research -- Conclusion and Prospective -- References. , Chapter 9 Quantitative Proteomic Approaches for Environmental Toxicology -- Abstract -- Introduction -- 1. Overview of Proteomic Techniques -- Conclusion and Prospective -- References -- Chapter 10 Toxin Proteomics for the Identification and Differentiation of Botulinum Neurotoxins -- Abstract -- Abbreviations -- Introduction -- Botulinum Neurotoxin Serotype Identification by Mass Spectrometry -- Neurotoxin-Associated Proteins Identification with Mass Spectrometry -- Serotype Detection of Bont in Complex Matrices -- Mass Spectrometry-Based Differentiation of Bont at the Subtype/Toxin Variant Level -- Conclusion and Future Directions -- References -- Chapter 11 Challenges of Mining Low to Medium Abundant Proteins for Proteomics -- Abstract -- 1. Introduction -- Removal of Contaminants -- Common Highly Abundant Proteins in Plant/Animal Tissues -- Removal of Highly Abundant Proteins in Plant/Animal Tissues -- Conclusion -- Acknowledgments -- References -- Index.