Applied Metallomics: From Life Sciences to Environmental Sciences

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Applied Metallomics: From Life Sciences to Environmental Sciences
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Contents
Foreword
Preface
1. Introduction
	1.1 A Brief Introduction to Metallomics
	1.2 Key Issues and Challenges in Metallomics
	1.3 About the Structure of this Book
	References
2. Nanometallomics
	2.1 The Concept of Nanometallomics
	2.2 The Analytical Techniques in Nanometallomics
		2.2.1 The Analytical Techniques for Size Characterization of Nanomaterials in Biological System
			2.2.1.1 Chromatography‐based Techniques for Size Characterization
			2.2.1.2 Mass‐spectrometry‐based Techniques for Size Characterization
			2.2.1.3 Laser, X‐rays, and Neutron‐beam‐based Techniques for Size Characterization
		2.2.2 The Analytical Techniques for Quantification of Nanomaterials and Metallome in Biological System
		2.2.3 The Analytical Techniques for Studying the Distribution of Nanomaterials in Biological System
		2.2.4 The Analytical Techniques for Studying the Metabolism of Nanomaterials in Biological System
	2.3 The Application of Nanometallomics in Nanotoxicology
		2.3.1 Understanding the Size Changes, Uptake and Excretion, Distribution, and Metabolism of Nanomaterials in Biological Systems
		2.3.2 Comparative Nanometallomics for Distinguishing Nanomaterials Exposure and Nanosafety Evaluation
	2.4 Conclusions and Perspectives
	Acknowledgments
	References
3. Environmetallomics
	3.1 The Concept of Environmetallomics
	3.2 The Analytical Techniques in Environmetallomics
		3.2.1 The Requirements for Environmetallome Analysis
		3.2.2 Quantitative Analysis for Environmetallomics
		3.2.3 Metal Distribution and Mapping for Environmetallomics
		3.2.4 Metal Speciation for Environmetallomics
		3.2.5 Metalloprotein Analysis
	3.3 The Application of Environmetallomics in Environmental Science and Ecotoxicological Science and the Perspectives
	Acknowledgments
	References
4. Agrometallomics
	4.1 The Concept of Agrometallomics
		4.1.1 Introduction
		4.1.2 Agrometallomics and its Concept
	4.2 Analytical Techniques in Agrometallomics
		4.2.1 Sensitivity and Multi‐elemental Analysis in Agrometallomics
			4.2.1.1 Mass Spectrometry in Agrometallomics
			4.2.1.2 Atomic Spectrometry for Agrometallomics
		4.2.2 Elemental Speciation and State Analysis in Agrometallomics
			4.2.2.1 Chromatographic Hyphenation for Atomic Spectrometry or Mass Spectrometry
			4.2.2.2 Synchrotron Radiation Analysis
			4.2.2.3 Energy Spectroscopy Based on X‐ray
		4.2.3 Spatial Distribution and Micro‐analysis Techniques in Agrometallomics
			4.2.3.1 Laser Ablation Inductively Coupled Plasma Mass Spectrometry
			4.2.3.2 Electrothermal Vaporization Hyphenation Technique
			4.2.3.3 Laser‐induced Breakdown Spectroscopy
			4.2.3.4 Single‐Cell and Micro‐particle Analysis
	4.3 Application and Perspectives of Agrometallomics in Agricultural Science and Food Science
		4.3.1 Agricultural Plants and Fungi and Derived Food
		4.3.2 Agricultural Animal and Derived Food
			4.3.2.1 Application of Sensitivity and Multielemental Analysis in Agricultural Animals
			4.3.2.2 Application of Elemental Speciation and State Analysis in Agricultural Animals
			4.3.2.3 Application of Spatial Distribution and Micro‐analysis in Agricultural Animals
		4.3.3 Soil, Water, and Fertilizer for Agriculture
	References
5. Metrometallomics
	5.1 The Concept of Metrometallomics
	5.2 The Analytical Techniques in Metrometallomics
		5.2.1 Analytical Techniques of Protein Quantification in Metrometallomics
		5.2.2 Analytical Techniques of Quantitative In Situ Analysis in Metrometallomics
	5.3 The Application of Metrometallomics in Life Science and the Perspectives
		5.3.1 Absolute Quantification of Metalloproteins in Metrometallomics
			5.3.1.1 Naturally Present Elements (P, S, Se, Metals)
			5.3.1.2 Elemental Labeling
			5.3.1.3 Directly Protein Tagging (I, Hg, Chelate Complexes)
			5.3.1.4 Immunological Tagging
			5.3.1.5 Direct Quantification of Proteins by LA‐ICP‐MS
			5.3.1.6 Calibration for Metalloprotein Quantification by ICP‐MS
			5.3.1.7 Perspectives of Absolute Quantification of Metalloproteins
		5.3.2 Calibration Strategies of Quantitative In Situ Analysis in Metrometallomics
			5.3.2.1 Internal Standardization
			5.3.2.2 External Calibration
			5.3.2.3 Calibration by Isotope Dilution
			5.3.2.4 Perspectives of Quantitative In Situ Analysis in Metrometallomics
	Acknowledgments
	References
6. Medimetallomics and Clinimetallomics
	6.1 The Concept of Medimetallomics and Clinimetallomics
		6.1.1 Medimetallomics
		6.1.2 Clinimetallomics
	6.2 The Analytical Techniques in Medimetallomics and Clinimetallomics
		6.2.1 Total Analysis of Clinical Elements
			6.2.1.1 Atomic Spectroscopy Detection Technology
			6.2.1.2 Mass Detection Technology
			6.2.1.3 Electrochemical Analysis
			6.2.1.4 Neutron Activation Analysis
		6.2.2 Clinical Element Morphology and Valence Analysis Technology
			6.2.2.1 Atomic Spectroscopy Detection Technology
			6.2.2.2 Mass Spectrometry Detection Technology
		6.2.3 Summary and Outlook
	6.3 The Application of Medimetallomics and Clinimetallomics in Medical and Clinical Science and the Perspectives
		6.3.1 Medimetallomics
			6.3.1.1 Global or National Medimetallomics Research
			6.3.1.2 Standardized Protocol for Medimetallomics Research
			6.3.1.3 The Application of Medimetallomics Results
			6.3.1.4 Next Steps and Opportunities for Medimetallomics
		6.3.2 Clinimetallomics
			6.3.2.1 Diseases Associated with Trace Elements
			6.3.2.2 Toxic‐Element‐Related Diseases
			6.3.2.3 Combined Toxicity of Multiple Heavy Metal Mixtures
			6.3.2.4 Genetic Diseases Associated with Metallomics
			6.3.2.5 Application of Metallomics in Disease Treatment
			6.3.2.6 Perspectives
	References
7. Matermetallomics
	7.1 The Concept of Matermetallomics
		7.1.1 Introduction
		7.1.2 Metallic Elements as Dopant
		7.1.3 Metallic Elements as Impurities
		7.1.4 Metallic Elements as Crosslinkers
	7.2 The Analytical Techniques in Matermetallomics
		7.2.1 Element Imaging Analysis
			7.2.1.1 Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA‐ICP‐MS)
			7.2.1.2 Laser‐Induced Breakdown Spectroscopy (LIBS)
			7.2.1.3 Secondary Ion Mass Spectrometry (SIMS)
			7.2.1.4 TEM/X‐EDS
			7.2.1.5 Synchrotron Radiation X‐Ray Fluorescence Spectrometry (SR‐XRF)
		7.2.2 Quantitative and Qualitative Analysis
			7.2.2.1 Inductively Coupled Plasma Atomic Emission Spectrometry (ICP‐AES)
			7.2.2.2 Inductively Coupled Plasma Mass Spectrometry (ICP‐MS)
			7.2.2.3 X‐Ray Fluorescence (XRF)
			7.2.2.4 GD Optical Emission Spectroscopy (GD‐OES) and GD Mass Spectrometry (GD‐MS)
		7.2.3 Metal Speciation Analysis
			7.2.3.1 Raman Spectroscopy
			7.2.3.2 X‐Ray Photo Electron Spectroscopy (XPS)
		7.2.4 Techniques Providing Depth Information
	7.3 The Application of Matermetallomics in Material Science and the Perspectives
		7.3.1 Matermetallomics in Semiconductor Materials
		7.3.2 Matermetallomics in Artificial Crystal Materials
	Acknowledgments
	References
8. Archaeometallomics
	8.1 The Concept of Archaeometallomics
	8.2 The Analytical Techniques in Archaeometallomics
		8.2.1 Neutron Activation Analysis (NAA)
		8.2.2 X‐Ray Fluorescence Analysis (XRF)
		8.2.3 Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA‐ICP‐MS)
		8.2.4 Laser‐induced Breakdown Spectroscopy (LIBS)
		8.2.5 Atomic Absorption Spectroscopy (AAS)
		8.2.6 X‐Ray Absorption Fine Structure Spectroscopy (XAFS)
		8.2.7 X‐Ray Diffraction (XRD)
		8.2.8 Neutron Diffraction
	8.3 The Application of Archaeometallomics in Archaeological Science
		8.3.1 The Application of Archaeometallomics in Ancient Ceramics
			8.3.1.1 Archaeometallomics in Studying the Origin and Dating of Ancient Ceramics
			8.3.1.2 Archaeometallomics in Studying the Color Mechanism and Firing Technology of Ancient Ceramics
		8.3.2 The Application of Archaeometallomics in Metal Cultural Relics
			8.3.2.1 Archaeometallomics in Studying the Origin of Metal Cultural Relics
			8.3.2.2 Archaeometallomics in Studying the Manufacturing Technology of Metal Cultural Relics
			8.3.2.3 Archaeometallomics in Studying the Corrosion of Metal Cultural Relics
		8.3.3 The Application of Archaeometallomics in Ancient Painting
			8.3.3.1 Archaeometallomics in Studying the Aging Mechanism of Painting Cultural Relics
			8.3.3.2 Archaeometallomics in Studying the Authenticity Identification of Painting Cultural Relics
	8.4 Summary and Perspectives
	Acknowledgments
	References
9. Metallomics in Toxicology
	9.1 Metallomic Research on the Toxicology of Metals
	9.2 Recent Progresses in Understanding the Health Effects of Heavy Metals
		9.2.1 Mercury, Oxidative Stress, and Cell Death
		9.2.2 Arsenic and Lung Cancer
		9.2.3 Epigenetic Effects of Cadmium
		9.2.4 Nephrotoxicity of Uranium in Drinking Water
	9.3 Knowledge Gaps, Challenges, and Perspectives
	Acknowledgments
	List of Abbreviations
	References
10. Pathometallomics: Taking Neurodegenerative Disease as an Example
	10.1 Introduction to Pathometallomics
		10.1.1 The Concept and Scope of Pathometallomics
		10.1.2 Brief Introduction to Methodologies for Pathometallomics
	10.2 Application of Pathometallomics in Neurodegenerative Diseases
		10.2.1 Pathometallomics in Alzheimer\'s Disease
			10.2.1.1 Dysregulation of Metal Homeostasis in AD
			10.2.1.2 Metal‐Associated Dysfunction in AD
			10.2.1.3 Application of Metallomics in the Prognosis of AD
			10.2.1.4 Metal Chelators as AD Therapeutics
		10.2.2 Pathometallomics in Parkinson\'s Disease
			10.2.2.1 Dysregulation of Metal Homeostasis in PD
			10.2.2.2 Application of Metallomics in the Prognosis of PD
			10.2.2.3 Application of Metallodrugs and Metalloproteins in the Treatment of PD
		10.2.3 Pathometallomics in Amyotrophic Lateral Sclerosis
			10.2.3.1 Dysregulation of Metal Homeostasis in ALS
			10.2.3.2 Metal‐Associated Dysfunction in ALS
		10.2.4 Pathometallomics in Autism Spectrum Disorder
	10.3 The Perspectives of Pathometallomics
	Acknowledgments
	References
11. Oncometallomics: Metallomics in Cancer Studies
	11.1 Introduction to Oncometallomics
	11.2 The Application of Oncometallomics in Cancer Studies
		11.2.1 The Application of Oncometallomics in Cancer Diagnosis
			11.2.1.1 Prostate Cancer
			11.2.1.2 Breast Cancer
			11.2.1.3 Lung Cancer
			11.2.1.4 Gastric Cancer
			11.2.1.5 Colorectal Cancer
			11.2.1.6 Esophageal Cancer
			11.2.1.7 Liver Cancer
			11.2.1.8 Ovarian Cancer
			11.2.1.9 Cervical Cancer
			11.2.1.10 Thyroid Cancer
		11.2.2 The Application of Oncometallomics in Cancer Treatment
	11.3 The Metallome that Involved in the Occurrence and Development of Cancer
	11.4 Conclusions and Perspectives
	Acknowledgments
	References
12. Bio-elementomics
	12.1 Introduction
		12.1.1 The Concept of Bio‐elementomics
		12.1.2 The Development History of Bio‐elementomics
		12.1.3 Research Scope
	12.2 Basic Laws of Bio‐elementomics
		12.2.1 Review of Bio‐elementomics
		12.2.2 Organizational Selectivity of Bio‐elements
		12.2.3 Specific Correlation of Bio‐elements
		12.2.4 Orderliness of Bio‐elements
		12.2.5 Diversity of Bio‐elements
		12.2.6 Biological Fractionation
		12.2.7 The Correlation Between the Bio‐elementomes and Other “Omes”
	12.3 Rare‐Earth Elementome
		12.3.1 Association of Rare‐Earth Elements and Related Diseases
		12.3.2 The Mechanism Studies of the Hormesis Effect of REEs Based on the Bio‐elementomics
		12.3.3 Beneficial Rebalancing Hypothesis for Hormesis Effect
	12.4 Limitations of Bio‐elementomics
		12.4.1 Statistically Higher Level of Some Elements in the Patient\'s Body
		12.4.2 Environment‐independent Biomarkers
		12.4.3 Trace Elements in Immortalized Lymphocytes
	12.5 Perspectives
		12.5.1 Speciation Analysis of Elements
		12.5.2 Bio‐elements and Their Interactions with Proteins, Genes, and Small Molecules
		12.5.3 Research Based on the Hormesis “Beneficial Rebalancing” Hypothesis
		12.5.4 Multi‐element Analysis of Immortalized Lymphocytes
		12.5.5 Analysis of Bio‐elements in Single Cell
	References
13. Methodology and Tools for Metallomics
	13.1 Brief Description of Metallomics
		13.1.1 Why Do Research on Biometals?
		13.1.2 What\'s the Goal of Metallomics?
		13.1.3 How to Perform a Metallomic Study?
	13.2 Methodologic Strategy for Metallomic Research
		13.2.1 In Vivo
		13.2.2 Ex Vivo
		13.2.3 In Vitro
		13.2.4 In Silico
	13.3 Tools for Metallomics
		13.3.1 Tools for Quantitative Metallomics
		13.3.2 Tools for Qualitative Metallomics
		13.3.3 Imaging Tools for Metallomics
	13.4 Concluding Remarks
	References
14. ICP-MS for Single-Cell Analysis in Metallomics
	14.1 Introduction
	14.2 ICP‐MS Instrumental Optimization for Single‐Cell Analysis
		14.2.1 Sample Introduction System
			14.2.1.1 Pneumatic Nebulization
			14.2.1.2 Laser Ablation
		14.2.2 Mass Analyzer and Detector
	14.3 Microfluidic Platform for Single‐Cells Analysis
		14.3.1 Droplet‐Encapsulation‐Based Single‐Cell Separation
		14.3.2 Hydrodynamic‐Capture‐Based Single‐Cell Separation
		14.3.3 Magnetic‐Separation‐Based Single‐Cell Capture
	14.4 ICP‐MS‐Based Single‐Cells Analysis in Metallomics
		14.4.1 Endogenous Elements in Single Cells
		14.4.2 Exogenous Metal Exposure to Single Cells
		14.4.3 Nanoparticles Uptake by Single Cells
		14.4.4 Metal‐containing Drugs Uptake by Single Cells
		14.4.5 Biomolecular Quantification at Single‐Cell Level
		14.4.6 Other Applications
	14.5 Summary and Perspectives
	References
15. Novel ICP-MS-based Techniques for Metallomics
	15.1 Introduction
	15.2 ICP‐MS: A Powerful Method in Metallomics
		15.2.1 Solution Introduction System and Plasma Source
		15.2.2 Time‐of‐flight Mass Analyzer
		15.2.3 Laser Ablation Systems
	15.3 Recent Advances in ICP‐MS‐based Metallomics
		15.3.1 Single‐particle Analysis
		15.3.2 Single‐cell Analysis
		15.3.3 Spatial Metallomics
	15.4 Conclusions
	Acknowledgment
	References
16. Machine Learning for Data Mining in Metallomics
	16.1 Data Mining Methods in Metallomics
		16.1.1 Data Preprocessing
			16.1.1.1 Smoothing Process
			16.1.1.2 Normalization
			16.1.1.3 Fourier Transform
			16.1.1.4 Wavelet Transform
			16.1.1.5 Convolution Operation
		16.1.2 Data Dimensionality Reduction
			16.1.2.1 Principal Component Analysis
			16.1.2.2 Independent Component Analysis
			16.1.2.3 Multidimensional Scaling
			16.1.2.4 Local Preserving Projection
			16.1.2.5 T‐Stochastic Neighbor Embedding
		16.1.3 Sample Set Division
			16.1.3.1 Random Sampling
			16.1.3.2 Kennard–Stone Sampling
			16.1.3.3 Sample Set Partitioning Based on Joint x−y Distances
			16.1.3.4 Cross‐Validation
			16.1.3.5 Leave‐One‐Out Cross Validation
		16.1.4 Predictive Model Building Method
			16.1.4.1 Partial Least Squares Regression
			16.1.4.2 Support Vector Machine
			16.1.4.3 Decision Tree
			16.1.4.4 K‐means Clustering
			16.1.4.5 Deep Learning
		16.1.5 Model Evaluation
			16.1.5.1 Evaluation Index of the Quantitative Model
			16.1.5.2 Evaluation Indicators of the Qualitative Model
	16.2 Application of Machine Learning for Data Mining in Metallomics
		16.2.1 Applications in Medical Science
		16.2.2 Applications in Agricultural Science
		16.2.3 Applications in the Environmental Science
	References
Index