Mass Spectrometry-Based Approaches for Treating Human Diseases and Diagnostics (Advances in Experimental Medicine and Biology, 1443)

Preface
Contents
Chapter 1: Isolation of Extracellular Vesicles Using Titanium Dioxide Microspheres
	1.1 Introduction
		1.1.1 Extracellular Vesicle Biosynthesis and Biological Functions in Diseases
		1.1.2 Omics Science Approaches for Extracellular Vesicle Characterization
	1.2 Material and Methods
		1.2.1 Plasma Samples
		1.2.2 Enrichment of Plasma EVs Using TiO2 Microspheres
		1.2.3 EV Morphological Characterization by Transmission Electron Microscopy and Nanoparticle Tracking Analysis (NTA)
			1.2.3.1 For NTA Analysis
			1.2.3.2 For TEM Analysis
		1.2.4 EV Plasma Proteome Identification Using MALDI-TOF MS and LC-MS/MS
			1.2.4.1 For the MALDI-TOF MS Approach
			1.2.4.2 For LC-MS/MS Analysis
		1.2.5 Bioinformatics Analysis of Mass Spectrometry-Based Proteomics (LC-MS/MS)
	1.3 Results of the EV Morphological Characterization and Proteome Identification
	1.4 Conclusion
	References
Chapter 2: Glycosort: A Computational Solution to Post-process Quantitative Large-Scale Intact Glycopeptide Analyses
	2.1 Introduction
		2.1.1 Glycosort: A Post-processing Tool for Large-Scale Quantitative Glycoproteomic Data
	2.2 Data Processing
	2.3 How to Use the Script
	2.4 Conclusions
	References
Chapter 3: Applications of Mass Spectrometry in the Characterization, Screening, Diagnosis, and Prognosis of COVID-19
	3.1 Introduction
	3.2 SARS-CoV-2: Understanding the Molecular Structure, the Mechanism of Viral Replication, and Pathogenesis
	3.3 MS-Based Analytical Approaches Provide Details on SARS-CoV-2 Molecular Structure and Virus-Host Interactions
	3.4 MS as a Major Tool for Understanding the Biological Properties of the Variants and Their Potential Impact on Public Health
	3.5 MALDI-TOF Mass Spectrometry in the Identification of Post-translational Modifications in SARS-CoV-2 and Other Viruses
	3.6 Mass Spectrometry-Based Approaches to Epitope Mapping: A Powerful Tool for Identifying the Specific Regions on a Protein That Are Recognized by the Immune System
	3.7 Clinical Peptidomics by MALDI-TOF-MS: Diagnosis and Prognosis
		3.7.1 Detection and Diagnosis
		3.7.2 Prognosis Models for COVID-19 Outcomes
	3.8 Optimization of Sample Preparation for Plasma Clinical Peptidomics by MALDI-TOF-MS
		3.8.1 MALDIquant General R Script
		3.8.2 Data Analysis with MALDIquant
	3.9 Final Considerations
	References
Chapter 4: Proteomics and Metabolomics in Congenital Zika Syndrome: A Review of Molecular Insights and Biomarker Discovery
	4.1 Introduction
	4.2 Zika Virus
		4.2.1 Epidemiology, Transmission, and Pathology
		4.2.2 ZIKV Composition
		4.2.3 Viral Cycle
			4.2.3.1 ZIKV Binding and Entry
			4.2.3.2 ZIKV Translation, Replication, and Assembly
			4.2.3.3 ZIKV Maturation and Secretion
		4.2.4 ZIKV Post-translational Modifications in Viral Pathogenicity
		4.2.5 Vertical Transmission
	4.3 Congenital Zika Syndrome
		4.3.1 Pathology and Diagnosis
		4.3.2 Blood-Brain Barrier
		4.3.3 In Vivo Models for CZS Studies
	4.4 Proteomics and Metabolomics Studies Applied to Congenital Zika Syndrome
		4.4.1 Mechanism for ZIKV Brain Infection and CZS Development
			4.4.1.1 Affinity Purification Coupled with Mass Spectrometry (AP-MS)
			4.4.1.2 Cross-Linking Coupled with Mass Spectrometry (XL-MS)
			4.4.1.3 Quantitative Proteomics and Metabolomics
				4.4.1.3.1 Proteomics Studies
				4.4.1.3.2 Metabolomics Studies
		4.4.2 PTMs Associated with ZIKV Brain Infection and CZS Development
		4.4.3 Precision Medicine and CZS Biomarkers
			4.4.3.1 Precision Medicine and Biomarker Concepts
			4.4.3.2 Biomarkers and MS-Based Proteomics
			4.4.3.3 CZS Biomarker Studies
	4.5 Conclusions
	References
Chapter 5: Mass Spectrometry Applications to Study Human Microbiome
	5.1 Impact of Human Microbiome on Health State
	5.2 Mass Spectrometry at a Glance
	5.3 Approaches for Dissecting the Functional Contribution of the Gut Microbiome to Metabolic Disease
	5.4 Mass Spectrometric Approaches Applied to Bacterial Identification
	5.5 Mapping Human Microbiome Drug Metabolism
	5.6 Conclusion and Future Perspectives
	References
Chapter 6: Neuroproteomics: Unveiling the Molecular Insights of Psychiatric Disorders with a Focus on Anxiety Disorder and Depression
	6.1 Introduction
	6.2 Anxiety Disorders
		6.2.1 Neurobiology
		6.2.2 Pharmacological Therapy of Anxiety Disorders
	6.3 Depression Disorders
		6.3.1 Neurobiology
		6.3.2 Pharmacological Therapy of Depressive Disorders
	6.4 Depression-like and Anxiety-like Animal Models and Tests
		6.4.1 Chronic Mild Stress
		6.4.2 Social Defeat
		6.4.3 Learned Helplessness
		6.4.4 Neonatal Maternal Separation
		6.4.5 Genetic Modification
	6.5 Behavioral Tests for Validation in Animal Models
		6.5.1 Open Field Test
		6.5.2 Forced Swim Test
		6.5.3 Light/Dark Box
		6.5.4 Sucrose Preference Test
	6.6 Omics Studies
		6.6.1 Omics of the Chronic Mild Stress Model
		6.6.2 Omics of the Social Defeat Model
		6.6.3 Omics of the Learned Helplessness Model
		6.6.4 Neonatal Maternal Separation Model
		6.6.5 Omics in the Genetic Modification Model
		6.6.6 Omics in Anxiety- and Depression-like Treatments
	6.7 Conclusions
	References
Chapter 7: Proteomic-Based Studies on Memory Formation in Normal and Neurodegenerative Disease-Affected Brains
	7.1 Introduction
	7.2 Memory
	7.3 Proteomics and Memory
	7.4 Proteomics and Neurodegenerative Disease
	7.5 Alzheimer’s Disease
	7.6 Parkinson’s Disease
	7.7 Conclusions
	References
Chapter 8: Cardioproteomics: Insights on Cardiovascular Diseases
	8.1 Introduction
	8.2 Atherosclerosis
		8.2.1 Endothelial Dysfunction
		8.2.2 Inflammation
		8.2.3 Calcification
	8.3 Coronary Artery Disease
		8.3.1 Myocardial Infarction
	8.4 Cardiomyopathy
		8.4.1 Hypertrophic Cardiomyopathy
		8.4.2 Dilated Cardiomyopathy
	8.5 Conclusions
	References
Chapter 9: Kidney Disease and Proteomics: A Recent Overview of a Useful Tool for Improving Early Diagnosis
	9.1 Introduction
	9.2 Diabetic Kidney Disease and Proteomics
	9.3 IgA Nephropathy and Proteomics
	9.4 Chronic Kidney Disease of Unknown Origin (CKDu) and Proteomics
	9.5 Autosomal Dominant Polycystic Kidney Disease (ADPKD) and Proteomics
	9.6 Lupus Nephritis and Proteomics
	9.7 Hypertensive Nephropathy and Proteomics
	9.8 COVID-19-Associated AKI and Proteomics
	9.9 Conclusions
	References
Chapter 10: Multi-omics Investigations in Endocrine Systems and Their Clinical Implications
	10.1 Proteomics in Diabetes Research
		10.1.1 Proteomics and Type 1 Diabetes
		10.1.2 Proteomics and Type 2 Diabetes
	10.2 Hypothalamic-Pituitary-Thyroid Axis
		10.2.1 The Use of Proteomic Approach in Studies of the HPT Axis
		10.2.2 Thyroid Cancer and Biomarkers
	10.3 Proteomics and the Reproductive System
		10.3.1 Network Controlling Male and Female Reproductive Systems
		10.3.2 Reproductive Tissue-Specific Proteome
		10.3.3 Proteomic Approach Within Infertility
		10.3.4 Proteomic Approach in Reproductive System Cancers
	10.4 Renin-Angiotensin System and Proteomics
	10.5 Omics and Circadian Rhythmicity
	10.6 Conclusion
	References
Chapter 11: Omics to Unveil Diabetes Mellitus Pathogenesis and Biomarkers: Focus on Proteomics, Lipidomics, and Metabolomics
	11.1 Introduction
	11.2 Omics in Diabetes Mellitus Diagnostics
		11.2.1 Proteomics
		11.2.2 Metabolomics
		11.2.3 Lipidomics
	11.3 Conclusions
	References
Chapter 12: Proteomics: Unraveling the Cross Talk Between Innate Immunity and Disease Pathophysiology, Diagnostics, and Treatment Options
	12.1 Introduction
	12.2 Infectious Diseases
		12.2.1 Diagnostics
		12.2.2 Treatment
	12.3 Cancer
		12.3.1 Diagnosis
		12.3.2 Treatment
	12.4 Autoimmune Diseases
		12.4.1 Diagnosis
		12.4.2 Treatment
	12.5 Neurodegenerative Diseases
	12.6 Conclusions
	References
Chapter 13: Applications of Proteomics in Probiotics Having Anticancer and Chemopreventive Properties
	13.1 Proteomics for Probiotic Traits
	13.2 Probiotics and Their Applications
	13.3 Proteomics for Anticancer Probiotics
		13.3.1 Proteomics for Anticancer Lactic Acid Bacteria
		13.3.2 Proteomics for Lactococcus lactis NCDO 2118
		13.3.3 Proteomics for Lactobacillus acidophilus
		13.3.4 Proteomics for Lactobacillus fermentum NCDC
		13.3.5 Proteomics for Surface-Exposed Proteins in Anticancer Probiotics
	13.4 Proteomics for Chemopreventive Probiotics
	13.5 Proteomics for Anti-inflammatory Probiotics
	13.6 Proteomics for Probiotic Formulations and Quality Control
	13.7 Conclusions
	References
Chapter 14: Mass Spectrometry-Based Characterization of Protein Aggregates in Tissues and Biofluids
	14.1 Introduction
	14.2 Methodology
		14.2.1 Isolation of Protein Aggregates
		14.2.2 Sample Preparation for Mass Spectrometry Analysis
		14.2.3 Mass Spectrometry Analysis
		14.2.4 Database Search
		14.2.5 Transmission Electron Microscopy (TEM) Analysis
		14.2.6 Western Blotting
	14.3 Results
		14.3.1 Aggregates Isolated from Human Plasma Show a Diversity of Protein Functions
		14.3.2 Neurodegeneration-Related Proteins and Exosomes Are Isolated in the Pellet Fraction of Human Plasma
		14.3.3 Isolated Protein Aggregates from Mouse Brain Are Composed of a Variety of Proteins Associated with Neurodegenerative Diseases
	14.4 Conclusions
	References
Index