Mass Spectrometry Imaging of Small Molecules: Methods and Protocols

Preface
Contents
Contributors
Part I: Innovations in Instrumental Methods for Mass Spectrometry Imaging
	Chapter 1: Gas-Phase Ion-Ion Reactions for Lipid Identification in Biological Tissue Sections
		1 Introduction
		2 Materials
			2.1 Tissue Cryosectioning
			2.2 Matrix Application by Sublimation
			2.3 Solution Preparation
			2.4 Instrumentation and Software
		3 Methods
			3.1 Tissue Sectioning
			3.2 Matrix Application
			3.3 Lipid Imaging Mass Spectrometry
			3.4 Ion/Ion Reactions Using Lipids Generated from Tissue
			3.5 Ion/Ion Reactions Using Lipid Standards
		4 Notes
		References
	Chapter 2: MALDI-2 and t-MALDI-2 Mass Spectrometry Imaging
		1 Introduction
		2 Materials
			2.1 Chemicals and Materials
				2.1.1 Tissues
				2.1.2 Cell Cultures
				2.1.3 Matrix Spray Preparation
				2.1.4 Matrix Sublimation Preparation
			2.2 Small Scale Instruments
			2.3 Mass Spectrometers
			2.4 Software
		3 Methods
			3.1 Tissue Preparation
			3.2 Cell Cultures
			3.3 Matrix Application
				3.3.1 Ultrasonic-Assisted Application of MALDI Matrix
				3.3.2 Sublimation Application of MALDI Matrix
			3.4 Data Acquisition
				3.4.1 MALDI-2 Imaging on the timsTOF fleX
				3.4.2 t-MALDI-2 Imaging on the Orbitrap Q Exactive Plus
			3.5 Image Processing
		4 Notes
		References
	Chapter 3: Ambient Mass Spectrometry Imaging of Small Molecules from Cells and Tissues
		1 Introduction
		2 Materials
			2.1 Materials for Atmospheric Pressure Mass Spectrometry Imaging (AP-MSI)
				2.1.1 Mass Spectrometry System
				2.1.2 Laser Desorption Source
				2.1.3 AP-Ionization Source: Nonthermal AP Helium Plasma Jet
				2.1.4 AP-Ionization Source: Electrospray Device
				2.1.5 Airflow-Assisted Particle Transport System
				2.1.6 Preparation of Hippocampal Brain Slices of Adult Mouse
				2.1.7 Preparation of Zebrafish Caudal Fin
				2.1.8 Preparation of Single Graphene Layer on Glass Substrate
				2.1.9 Software for AP-MSI
			2.2 Materials for SIMS Imaging of Untreated Wet Cells in Solution Capped by Single-Layer Graphene
				2.2.1 Cell Culture Wet Substrate
				2.2.2 Graphene Capping
		3 Methods
			3.1 Methods for Atmospheric Pressure Mass Spectrometry Imaging (AP-MSI)
				3.1.1 Basic Arrangement of Mass Spectrometer System
				3.1.2 Installation of Laser Desorption Source
				3.1.3 Installation of AP-Ionization Source: Nonthermal AP Helium Plasma Jet
				3.1.4 Setup of Airflow-Assisted Particle Transport System
				3.1.5 Installation of AP-Ionization Source: Electrospray Ionization Equipment
				3.1.6 Setup of Programmable Scanning Stage
				3.1.7 Preparation of Hippocampal Tissue Slices of Adult Mouse with Nanomaterial Treatments
				3.1.8 Preparation of Hippocampal Tissue Slices on Graphene Coated Glass Substrate
				3.1.9 Preparation of Zebrafish Caudal Fin
				3.1.10 Data Acquisition
				3.1.11 MS Raw Data Conversion to imzML Format
				3.1.12 Chemical Mapping Information of MSI and Tentative Mass Assignment
			3.2 Methods for SIMS Imaging of Untreated Wet Cells in Solution Capped by Single-Layer Graphene
				3.2.1 Fabrication of a Cell Culture Wet Substrate (Fig. 6)
				3.2.2 Graphene Capping (Fig. 7)
				3.2.3 ToF-SIMS Imaging
		4 Notes
		References
	Chapter 4: Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures
		1 Introduction
		2 Materials
			2.1 Reagents and Chemicals
			2.2 Biological Samples and Associated Tools
			2.3 f-LAESI Components
				2.3.1 Laser Pulse Delivery
				2.3.2 Electrospray
				2.3.3 Visualization System
				2.3.4 Sample Stage Components
			2.4 Ultrahigh Mass Resolution Mass Spectrometer
			2.5 Data Analysis
		3 Methods
			3.1 Sample Preparation for Single Cell Analysis
			3.2 Fabrication of Optical Fiber
			3.3 f-LAESI Source Setup and Laser-Pulse Delivery
			3.4 FTICR-MS Data Acquisition
			3.5 Metabolite Assignments by Ultrahigh Mass Accuracy and Isotope Fine Structure
				3.5.1 Accurate Mass and IFS Library Generation for Known Compounds
				3.5.2 Mass Spectra Processing and Rapid Assignments of Known Compounds by IFS
				3.5.3 Elemental Composition Assignments for Unknown Compounds by IFS
		4 Notes
		References
	Chapter 5: TOF-SIMS Imaging of Biological Tissue Sections and Structural Determination Using Tandem MS
		1 Introduction
		2 Materials
			2.1 Chemicals and Materials
			2.2 Instrumentation
		3 Methods
			3.1 Tissue Sectioning
			3.2 Tissue Staining
			3.3 Sample Preparation Prior to ToF-SIMS
			3.4 ToF-SIMS Imaging
			3.5 Hybrid SIMS MS/MS
		4 Notes
		References
Part II: New Types of Laser Absorption Methods in Mass Spectrometry Imaging
	Chapter 6: Mass Spectrometry Imaging of Biological Tissues by Laser Desorption Ionization from Silicon Nanopost Arrays
		1 Introduction
		2 Materials
			2.1 Biological Samples
			2.2 NAPA Imaging Chips
			2.3 Sample-Preparation
			2.4 Mass Spectrometer and Associated Supplies
			2.5 Software for Data Analysis
		3 Methods
			3.1 Sample Preparation for NAPA-LDI-MSI
			3.2 NAPA-LDI-MSI
			3.3 Mass Spectra and Chemical Image Analysis
		4 Notes
		References
	Chapter 7: Metal-Assisted Laser Desorption Ionization Imaging Mass Spectrometry
		1 Introduction
		2 Materials
			2.1 Tissue Section Preparation
			2.2 Salt Pneumatic Spray Deposition
			2.3 Metal Sputter Deposition
			2.4 LDI IMS Data Acquisition
		3 Methods
			3.1 Tissue Sectioning
			3.2 Tissue Sections Use and Preservation
			3.3 Salt Spray Deposition
			3.4 Metal Sputter Deposition
			3.5 Metal-Assisted LDI IMS Data Acquisition
			3.6 Analysis of AgLDI and AuLDI IMS Datasets
		4 Notes
		References
	Chapter 8: Mass Spectrometry Imaging of Metabolites by Nanostructure Initiator Mass Spectrometry with Fluorinated Gold Nanopar...
		1 Introduction
		2 Materials
			2.1 f-AuNPs Preparation
			2.2 Silicon Plate Preparation
			2.3 Sample Preparation
			2.4 Instrumentation
			2.5 Software and Spectral Databases
		3 Methods
			3.1 f-AuNPs Synthesis
			3.2 Silicon Plate Preparation
			3.3 Sample Preparation
			3.4 MSI Analysis
			3.5 Data Processing and Interpretation
		4 Notes
		References
	Chapter 9: Imaging of Plant Hormones with Nanoparticle-Assisted Laser Desorption/Ionization Mass Spectrometry
		1 Introduction
		2 Materials
			2.1 Materials for Plant Growth
			2.2 Nanoparticle Synthesis
			2.3 Mass Spectrometry Imaging
		3 Methods
			3.1 Plant Growth
			3.2 Preparation and Characterization of NPs
			3.3 Synthesis of Organic Matrix-Modified NPs
			3.4 Test MS Measurement of Standard Samples
			3.5 Tissue Sample Preparation
			3.6 Application of Nanoparticles or Organic Matrix on Sections (Fig. 5)
			3.7 MS Imaging of Plant Root
		4 Notes
		References
Part III: Quantitative Mass Spectrometry Imaging
	Chapter 10: Nanosecond Photochemical Reaction (nsPCR) for Enhanced Mass Spectrometric Identification, Quantification, and Visu...
		1 Introduction
		2 Materials
			2.1 The nsPCR Reagents
			2.2 Other Reagents and Analytes
			2.3 Apparatus and Instrumentation
		3 Methods
			3.1 Sample Preparation for Spot Analysis (Steps 1 and 2, Fig. 2)
			3.2 Sample Preparation for Imaging Analysis (Steps 1 and 2, Fig. 3)
				3.2.1 nsPCR Reagent Preparation for Imaging Analysis
				3.2.2 Tissue Sample Preparation
				3.2.3 Matrix and nsPCR Reagent Application to Tissues
			3.3 nsPCR MS Operations
				3.3.1 MS Operation for nsPCR-Enabled Spot Analysis (Step 3, Fig. 2)
				3.3.2 MS Operation for nsPCR-Enabled Imaging Analysis (Step 3, Fig. 3)
			3.4 nsPCR Data Analysis
				3.4.1 Data Analysis for nsPCR-Enabled Spot Analysis (Step 4, Fig. 2)
				3.4.2 Data Analysis for nsPCR-Enabled Imaging Analysis (Steps 4 and 5, Fig. 3)
		4 Notes
		References
	Chapter 11: Extraction and Upconcentration of Adsorbates from Precisely Defined Area for Quantitative MALDI Mass Spectrometry ...
		1 Introduction
		2 Materials
			2.1 Preparation of Microstructured PDMS Stamp
			2.2 Solvent and Reagents
			2.3 Instrumentation
			2.4 Software
		3 Methods
			3.1 Fabrication of Microstructured PDMS Stamp
			3.2 Analyte Extraction by Matrix Crystal Arrays
			3.3 Preparation of Calibration Standards
			3.4 MALDI-MSI and Data Analysis
		4 Notes
		References
	Chapter 12: Development and Application of DropletProbe Mass Spectrometry for Examining Biodistribution of Therapeutics
		1 Introduction
		2 Materials
			2.1 Chemicals
			2.2 Animal
			2.3 Equipment
			2.4 Miscellaneous
		3 Methods
			3.1 Animal Experiments and Whole-Body Section Preparation
			3.2 Surface Sampling
			3.3 HPLC-MS Analysis
		4 Notes
		References
	Chapter 13: Quantitative Mass Spectrometry Imaging with Liquid Microjunction Surface Sampling
		1 Introduction
		2 Materials
			2.1 LMJSS Extraction Solvents
			2.2 Flow-Probe
			2.3 LC-MS System
		3 Methods
			3.1 Assembly of LMJSS
			3.2 Mass Spectrometry Imaging with LMJSS
			3.3 Analytical Conditions for MS or UPLC-MS
			3.4 Quantitation Method for LMJSS with Complete Extraction
			3.5 Quantitation Method for LMJSS with Incomplete Extraction
			3.6 Reconstruction of Heatmaps
		4 Notes
		References
Part IV: New Types of Applications
	Chapter 14: Enhancing Metabolite Coverage for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Through Mu...
		1 Introduction
		2 Materials
			2.1 Cryosectioning
			2.2 Tissue Drying
			2.3 Derivatization and Matrix Application Via TM Sprayer
			2.4 Derivatization Application Via ESI Deposition
			2.5 Matrix Application Via Sputter Coater
		3 Methods
			3.1 Tissue Sectioning
			3.2 Tissue Drying
			3.3 On-Tissue Derivatization with TM Sprayer
			3.4 Derivatization Application Via ESI Deposition
			3.5 Matrix Application Via Sputter Coater
			3.6 Matrix Application Via TM Sprayer
			3.7 Data Acquisition
			3.8 Analysis of Derivatized Data Sets
		4 Notes
		References
	Chapter 15: Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Glycogen In Situ
		1 Introduction
		2 Materials
			2.1 General Materials and Equipment
			2.2 Reagents
			2.3 Solutions
			2.4 Optional Materials
			2.5 Mouse Information
		3 Methods
			3.1 Preparation of Formalin-Fixed, Paraffin-Embedded (FFPE) Tissue Sections
			3.2 Desalt Isoamylase
			3.3 Dewax FFPE Slides
			3.4 Antigen Retrieval
			3.5 Isoamylase Application
			3.6 Matrix Application
			3.7 MALDI-MSI Settings
		4 Notes
		References
	Chapter 16: MALDI Mass Spectrometry Imaging of Lipids on Free-Floating Brain Sections and Immunohistochemically Colocalized Ma...
		1 Introduction
		2 Materials
			2.1 Paraformaldehyde-Fixed Free-Floating Sections
			2.2 Sample Preparation for MSI
			2.3 Immunohistochemistry
			2.4 Instruments and Software
		3 Methods
			3.1 Fixation and Sectioning
			3.2 MALDI MSI
				3.2.1 Sample Preparation for MALDI MSI
				3.2.2 Matrix Deposition for MALDI MSI
				3.2.3 MALDI MSI Measurement and Analysis
			3.3 Immunohistochemistry Staining
			3.4 The Colocalization of Images Acquired from MALDI MSI and Confocal Microscope
		4 Notes
		References
	Chapter 17: Silver-Doped Nano-DESI MSI for Increased Specificity and Sensitivity of Alkenes
		1 Introduction
		2 Materials
			2.1 Solvent
			2.2 Nano-DESI
			2.3 Sample Preparation
		3 Methods
			3.1 Preparation of Sample
			3.2 Preparation of Solvent
				3.2.1 Preparation of Monoisotopic AgNO3 (Optional)
				3.2.2 Preparation of Silver-Doped Nano-DESI Solvent
			3.3 Nano-DESI Setup
				3.3.1 Secondary Capillary
				3.3.2 Primary Capillary
				3.3.3 Setting Up the Nano-DESI by the Mass Spectrometer
				3.3.4 Running the Imaging Experiment
				3.3.5 Mass Spectrometry Method and Data Analysis
		4 Notes
		References
Part V: Innovations in Data Analysis
	Chapter 18: Extract Metabolomic Information from Mass Spectrometry Images Using Advanced Data Analysis
		1 Introduction
		2 Materials
		3 Method
			3.1 Data Preprocessing
			3.2 Multivariate Curve Resolution Alternating Square
			3.3 Unsupervised Machine Learning
				3.3.1 Cluster Large Applications
				3.3.2 Density-Based Spatial Clustering of Applications with Noise
			3.4 Supervised Machine Learning
			3.5 Image Fusion
		4 Notes
		References
Index