Front Cover; Proteomics in Biology, Part B; Copyright; Contents; Contributors; Preface; Chapter One: Protein Cysteinyl-S-Nitrosylation: Analysis and Quantification; 1. Introduction; 2. SNOFlo Methodology; 3. Applications; References; Chapter Two: Quantitative Proteomics of the E. coli Membranome; 1. Introduction-Pipeline Overview; 2. Sample Preparation; 2.1. Introduction; 2.2. Preparation of IMVs; 2.3. MS Sample Preparation; 2.3.1. Surface Proteolysis Protocol; 2.3.2. SDS-PAGE and In-Gel Digestion Protocol; 2.3.3. Desalting of Peptides Using C18 Tips.

2.3.4. Additional Proteomics Sample Preparation Methods3. Peptide/Protein Identification; 3.1. Introduction; 3.2. MS Analysis; 3.3. Peptide/Protein Identification; 3.3.1. Peptide Identification-Approach 1; 3.3.2. Peptide Identification-Approach 2; 4. Quantification; 4.1. Introduction; 4.2. Spectral-Based Quantification of Membrane Proteins; 4.3. Intensity-Based Label-Free Quantification of Membrane Proteins; 4.3.1. Peptide Intensity Normalization; 4.3.2. Quantification and Statistical Analysis; 4.3.2.1. Univariate Analysis; 4.3.2.2. Multivariate Analysis; 5. Functional Annotation.

6. ConclusionAcknowledgments; References; Chapter Three: Comparative Analysis and Validation of Different Steps in Glycomics Studies; 1. Introduction; 2. Experimental Design and Randomization; 2.1. Sample Randomization; 3. Sample Preparation for UPLC N-Glycan Analysis; 3.1. IgG Isolation From Plasma/Serum; 3.2. N-Glycan Release; 3.3. Labeling of Free N-Glycans With 2-Aminobenzamide; 3.4. Cleanup of 2-AB-Labeled N-Glycans; 4. Robustness of the Sample Preparation Method; 5. Analysis of Sources of Variation; 6. Method Validation (Between-Day and Between-Analyst Variation).

7. UPLC Analysis of 2-AB-Labeled N-Glycans7.1. Validation of UPLC Method for IgG N-Glycan Analysis; 8. Data Analysis and Quality Control; 9. Summary and Conclusions; Acknowledgments; References; Chapter Four: Analysis of Translocation-Competent Secretory Proteins by HDX-MS; 1. Introduction; 2. Preparation of Polypeptides; 2.1. Isolation of Translocation-Competent and Native Protein States; 2.2. Protein Preparation for HDX; 3. Isotope Labeling; 3.1. Pulsed HDX on Translocation-Competent and Native Protein States; 3.2. Preparation of Unlabeled and Complete Deuteration Controls.

4. Mass Spectrometric Analysis4.1. Online Proteolytic Digestion and LC-MS Analysis; 4.2. Data Analysis; 4.2.1. Peptide Identification; 4.2.2. Deuterium Uptake Determination; 5. Data Visualization and Interpretation; 6. Identifying Statistically Significant Conformational Differences in Comparative Local HDX-MS; 7. Conclusions; Acknowledgments; References; Chapter Five: Site-Specific Quantification of Lysine Acetylation Using Isotopic Labeling; 1. Introduction; 2. Principle of Site-Specific Quantification of Lysine Acetylation Using Isotopic Labeling; 3. Experimental Procedures.