Imaging Mass Spectrometry: Methods and Protocols

Preface
Contents
Contributors
Chapter 1: MALDI and Trace Metal Analysis in Age-Related Macular Degeneration
1 Introduction
2 Materials
2.1 MALDI Analysis
2.2 LA-ICP-MS Analysis
2.3 Software for Data Analysis
2.4 Reagents: Working Composition
3 Methods
3.1 Slide Preparation
3.2 Enzyme Application
3.3 Matrix Application
3.4 Sample Storage
3.5 MALDI Data Acquisition
3.6 Matrix Washing
3.7 Calibration Arrays
3.8 Data Analysis
3.9 ICP-MS
3.10 Quantitative ICP
3.11 Laser Ablation
4 Results
5 Conclusions
6 Notes
References
Chapter 2: HistoSnap: A Novel Software Tool to Extract m/z-Specific Images from Large MSHC Datasets
1 Introduction
2 Materials and Methods
2.1 Samples
2.2 Data Acquisition
2.3 Software Implementation
3 HistoSnap Operation Sequence
4 Discussion
5 Notes
References
Chapter 3: Spatially Resolved Quantitation of Drug in Skin Equivalents Using Mass Spectrometry Imaging (MSI)
1 Introduction
2 Materials
2.1 Tissue Treatment
2.2 Tissue Washing
2.3 Tissue Freezing (Cryopreservation)
2.4 Tissue Sectioning
2.5 Tissue Drying
2.6 Analytical and Internal Standards
2.7 Matrix Coating
2.8 MS Setup and Data Acquisition
2.9 Software Processing
3 Methods
3.1 Sample Handling
3.2 Cryo-conservation of Tissue
3.3 Cryo-sectioning of Tissue
3.4 Calibration Curve Construction
3.5 Acoustic Spotter Portrait 630: Application of Internal Standard onto the Treated Samples
3.6 Matrix Application
3.7 Instrumentation and Data Acquisition
3.8 Data Analysis
4 Notes
References
Chapter 4: Update DESI Mass Spectrometry Imaging (MSI)
1 Introduction
2 Materials
2.1 Tissue Sections
2.2 Reagents
2.3 Equipment
2.4 Software
3 Methods
3.1 Sprayer Construction
3.2 DESI Signal Optimization
3.3 Mass Calibration Using the DESI Source
3.3.1 Preparation of the Polyalanine Thin Film Sample
3.3.2 MS Calibration
3.4 DESI Imaging Setup
3.5 Maintenance
3.5.1 Cleaning of the HP DESI Sprayer Emitter Cartridge and Nozzle
3.5.2 Cleaning of the Ion Inlet Tube
3.5.3 Cleaning of the Heated Transfer Line (HTL)
4 Notes
References
Chapter 5: Liquid Extraction Surface Analysis Mass Spectrometry Imaging of Denatured Intact Proteins
1 Introduction
2 Materials
2.1 Tissue Sample Preparation
2.2 LESA Solvents
2.3 Analysis
3 Methods
3.1 Preparation of Tissue Sample
3.2 Liquid Extraction Surface Analysis
3.3 Mass Spectrometry
3.4 Visualizing Mass Spectrometry Imaging Data
4 Notes
References
Chapter 6: MALDI MS Imaging of Cucumbers
1 Introduction
2 Materials
2.1 Preparation of Cucumber Sections
2.2 Matrix Deposition
3 Methods
3.1 Cucumber Preparation
3.2 Preparation of Aluminum Substrate
3.3 Matrix Deposition
3.3.1 Matrix Deposition: Spraying
4 Notes
References
Chapter 7: The Adaptation of the QV600 LLI Milli-Fluidics System to House Ex Vivo Gastrointestinal Tissue Suitable for Drug Ab...
1 Introduction
2 Materials
2.1 QV600 LLI Setup
2.2 Fresh Tissue Collection
2.3 Fresh Tissue Preparation
2.4 QV600 LLI Experiment Setup
2.5 Snap-Freezing Disks of Tissue from QV600 LLI
2.6 Cleaning QV600 LLI
2.7 Cryosectioning Disks of Tissue
2.8 MALDI Matrix Application
2.9 Preparation of Samples for LC-MS/MS Analysis
2.10 Software
2.11 Instrumentation
3 Methods
3.1 QV600 LLI Setup
3.2 Fresh Tissue Collection and Transport
3.3 Fresh Tissue Preparation and QV600 LLI Experiment Setup
3.4 Stopping the Experiment and Emptying the QV600 LLI
3.5 Snap-Freezing Disks of Tissue from QV600 LLI
3.6 Cleaning QV600 LLI
3.7 Cryosectioning Disks of Tissue
3.8 MALDI Matrix Application
3.9 MALDI MS Imaging
3.10 Preparation of Samples for LC-MS/MS Analysis
3.11 LC-MS/MS
4 Notes
References
Chapter 8: Ambient Mass Spectrometry Imaging by Water-Assisted Laser Desorption/Ionization for Ex Vivo and in Vivo Applications
1 Introduction
2 Materials
2.1 Preparation of Snap Frozen Tissues
2.1.1 Snap Freezing
2.1.2 Tissue Cryo-Sectioning
2.2 Preparation of FFPE Tissue Sections
2.2.1 Tissue Sectioning
2.2.2 Glycerol Deposition
2.3 WALDI Mass Spectrometry Imaging Analysis
2.4 Data Analysis
2.4.1 Image co-Registration
2.4.2 Data Processing with SCiLS
3 Methods
3.1 Preparation of Fresh Tissues
3.2 Preparation of Fresh-Frozen Section
3.2.1 Snap Freezing
3.2.2 Tissue Sectioning
3.3 Formalin-Fixed Paraffin-Embedded (FFPE) Tissues
3.3.1 Tissue Sectioning
3.3.2 Glycerol Spray Deposition
3.4 Mass Spectrometry Imaging Analysis
3.4.1 2D Imaging of Tissue Sections
3.4.2 3D and in Vivo Imaging
3.4.3 MS/MS Analysis
3.5 Image Reconstructions
3.5.1 Plotting M/z Images onto 2D and 3D Topographical Maps
3.5.2 Importation of 2D Images into SCiLS Software
References
Chapter 9: Cytological Cytospin Preparation for the Spatial Proteomics Analysis of Thyroid Nodules Using MALDI-MSI
1 Introduction
2 Materials
2.1 Instrumentation
2.2 Software
3 Methods
3.1 Sample Collection
3.2 Cytospin Sample Preparation and Stocking
3.3 Sample Preparation for MALDI-MSI
3.4 MALDI-MSI Analysis
3.5 Cytological Evaluation
3.6 Data Elaboration
4 Notes
References
Chapter 10: Matrix Effects Free Imaging of Thin Tissue Sections Using Pneumatically Assisted Nano-DESI MSI
1 Introduction
2 Materials
2.1 Solvent
2.2 Pneumatically Assisted Nano-DESI
2.3 Preparation of Sample
3 Methods
3.1 Thin Tissue Section Preparation
3.2 Preparation of PA Nano-DESI Solvent
3.2.1 Identification and Use of Appropriate Internal Standards
3.2.2 Preparation of Doped PA Nano-DESI Solvent with Internal Standards
3.2.3 Crown Ethers for Determining Alkali Metal Ion Changes
3.3 Pneumatically Assisted Nano-DESI Setup
3.3.1 Construction of the Nebulizer Device for the Secondary Capillary
3.3.2 Construction of the Primary Capillary
3.3.3 Setting Up the PA Nano-DESI
3.3.4 Setting Up and Running the Imaging Experiment
3.3.5 Mass Spectrometry Method
3.3.6 Data Normalization and Relative Quantification
4 Notes
References
Chapter 11: Laser Ablation Inductively Coupled Plasma Mass Spectrometry Imaging of Plant Materials
1 Introduction
2 Materials
2.1 Materials for Preparation of Leaf Material
2.2 Materials for Embedding of Seed Material in CMC/Gelatin
2.3 Materials for the Preparation of Matrix-Matched Standards
3 Methods
3.1 Leaf Material for Imaging
3.2 Sample Preparation for CMC/Gelatin Embedding
3.3 Cryosectioning and Embedding of Seeds
3.4 Embedding of Seeds in Epoxy Resin
3.5 LA Matrix-Matched Standard Preparation
3.6 Optimization of LA Parameters for Bioimaging
3.6.1 Laser Spot Size
3.6.2 Laser Spot Shape
3.6.3 Laser Power
3.6.4 Laser Repetition Rate
3.6.5 Laser Scan Rate
3.6.6 Sample Chamber Washout Time
3.7 Calculating the Spatial Resolution of LA-ICP-MS Images
3.7.1 Calculating the Spatial Resolution in the X Direction
3.7.2 Calculating the Spatial Resolution in the Y Direction
3.8 Production of Elemental Distribution Maps
4 Notes
References
Chapter 12: Sample Preparation for Metabolite Detection in Mass Spectrometry Imaging
1 Introduction
2 Materials
2.1 Tissue Cryosectioning
2.2 Vacuum Drying and Packing
2.3 Matrix Application
3 Methods
3.1 Cryosectioning
3.2 Vacuum Drying and Packing
3.3 Matrix Application
4 Notes
References
Chapter 13: Multimodal Mass Spectrometry Imaging of an Aggregated 3D Cell Culture Model
1 Introduction
2 Materials
2.1 Aggregated 3D Culturing Growth
2.2 Tissue Embedding
2.3 Tissue Sectioning
2.4 Sample Preparation
2.4.1 IMC Staining
2.5 Histological Analysis
3 Methods
3.1 Aggregoid Formation
3.2 Tissue Embedding
3.3 Tissue Sectioning
3.4 MSI Analysis
3.4.1 DESI-MSI Acquisition
3.4.2 IMC Sample Preparation and Acquisition
3.4.3 La-ICP-MSI
3.5 Histology
4 Notes
References
Chapter 14: Visualization of Small Intact Proteins in Breast Cancer FFPE Tissue
1 Introduction
2 Materials
2.1 Tissue Sectioning
2.2 Tissue Washing
2.3 Antigen Retrieval
2.4 Matrix Application
2.5 MALDI MSI Analysis
3 Methods
3.1 FFPE Tissue Sectioning
3.2 Dewaxing and Washing
3.3 Antigen Retrieval
3.4 Matrix Application
3.5 MALDI MSI
4 Notes
References
Chapter 15: Negative Ion-Mode N-Glycan Mass Spectrometry Imaging by MALDI-2-TOF-MS
1 Introduction
2 Materials
2.1 Instruments and Glassware
2.2 Cleaning, Coating, and Marking Glass Slides
2.3 Poly-L-lysine Coating Solution
2.4 Solutions for Paraffin Removal and Rehydration (see Note 2)
2.5 Fiducial Markers and Pre-MSI Optical Image
2.6 PNGase F Buffer Exchange
2.7 In Situ Enzymatic N-Glycan Release
2.8 Matrix and Internal Standard Application
2.9 External Instrument Calibration
2.10 Software for Data Acquisition
3 Methods
3.1 Marking, Cleaning, and Coating Glass Slides
3.2 Sectioning Formalin-Fixed Paraffin-Embedded Tissues
3.3 Paraffin Removal and Rehydration
3.4 Fiducial Markers and Pre-MSI Optical Image
3.5 PNGase F Buffer Exchange
3.6 In Situ Enzymatic N-Glycan Release
3.7 Matrix and Internal Standard Application
3.8 Spotting External Calibrant
3.9 Setting Up MALDI-2-MS Method
3.10 Setting Up the MALDI-MSI Analysis
4 Notes
References
Chapter 16: MS1-Based Data Analysis Approaches for FFPE Tissue Imaging of Endogenous Peptide Ions by Mass Spectrometry Histoch...
1 Introduction
2 Materials and Methods
2.1 Tissue Selection
2.2 Sample Preparation
2.3 Data Analysis
3 Results and Discussion
3.1 Histology-Guided Region of Interest (ROI) Selection
3.2 Mass Accuracy and Post-acquisition Mass Recalibration
3.3 Identification of Peptide-Like Features by Kendrick Mass Defect Filtering
3.4 Isotopic Distribution of Known Peptides and Peptide-Like Features
3.5 Co-localization of Vasopressin and Oxytocin with IHC Data
3.6 Identification of Peptide Adducts and Chemically or Post-translationally Modified Peptides
3.7 Identification of Ions of Analytes Other Than Peptides
3.8 Co-localization of Neuropeptide and Other Ions with Identified Tissue Features
References
Chapter 17: Perspective: Mass Spectrometry Imaging - The Next 5 Years
1 Introduction
2 Technical Advances
2.1 Ionization Suppression
2.2 Sample Throughput
2.3 Imaging Low-Abundance Proteins/Targeted Imaging
3 Emerging Applications of MSI
3.1 Native Proteins
3.2 3D Tissue Models
4 Data Handling
4.1 Use of AI to Convert MSI Data to Information
5 Conclusions
References
Index