Jun 25, 2024
NEDC matrix application for metabolite imaging using MALDI-MSI
- Antonia Fecke1,
- Karl W Smith1,
- Siva Swapna Kasarla1,
- Philipp Bäuml1,
- Prasad Phapale2
- 1Leibniz Institut für analytische Wissenschaften - ISAS - e.V., Dortmund, Germany;
- 2ISAS Dortmund
- Antonia Fecke: Spatial Metabolomics;
- Karl W Smith: Spatial Metabolomics
- Siva Swapna Kasarla: Spatial Metabolomics
- Philipp Bäuml: Spatial Metabolomics
- Metabolomics Protocols & WorkflowsTech. support email: [email protected]
Protocol Citation: Antonia Fecke, Karl W Smith, Siva Swapna Kasarla, Philipp Bäuml, Prasad Phapale 2024. NEDC matrix application for metabolite imaging using MALDI-MSI. protocols.io https://dx.doi.org/10.17504/protocols.io.ewov1q28kgr2/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 22, 2023
Last Modified: June 25, 2024
Protocol Integer ID: 88193
Keywords: nedc matrix application for metabolite imaging, metabolite imaging, metabolomics research, untargeted metabolomic, msi of metabolite, ionization mass spectrometry, mass spectrometry, study of metabolite, small molecules such as metabolite, imaging tool for biological tissue, molecules within complex tissue sample, broad range of metabolite, potential links between metabolite variation, metabolome coverage, investigation of metabolic pathway, biological tissue imaging, fresh frozen tissue samples for maldi, metabolite variation, metabolic pathway, metabolite, biomarker, spectrometry, complex tissue sample, large biomolecule, metabolic change, using maldi, tissue sample, msi matrix, preparation of tissue sample, metabolome coverage within different type, large biomolecules like protein, imaging tool, peptide, correlation of metabolic change, maldi
Funders Acknowledgements:
Funding: This work was funded by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF) under the funding reference 161L0271 and supported by the Ministry of Culture and Science of the State of North Rhine-Westphalia (Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen, MKW NRW)
Grant ID: 161L0271
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has emerged as a analytical technique more than 30 years ago. Originally developed as a method to analyze large biomolecules like proteins or peptides, MALDI-MS has over the years found a new application in the field of biological tissue imaging (MALDI-MSI).
MALDI-MS has been utilized as an imaging tool for biological tissues, giving insight into the spatial distribution of molecules within complex tissue samples. Metabolomics research, which focuses on the study of metabolites present in a biological system, can benefit from this technology.
Small molecules such as metabolites or lipids can be analyzed under the aspect of spatial distribution across tissue sections. This enables the investigation of metabolic pathways, biomarkers or the correlation of metabolic changes with specific tissue regions, uncovering potential links between metabolite variations and physiological or pathological conditions.
Despite its potential, untargeted metabolomics using MALDI-MSI still faces several limitations. One major challenge is the diversity of matrices and protocols which are used to enhance ionization efficiency and the lack of information on metabolome coverage within different types of methods. One matrix of interest is NEDC (N-(1-napthyl)ethylendiamine dihydrochloride), which has gained recognition for its efficiency to visualize a broad range of metabolites.
This protocol provides a guide on how to prepare fresh frozen tissue samples for MALDI-MSI of metabolites using the NEDC matrix. It covers cryosectioning and preparation of tissue samples and provides a method for NEDC matrix application using the Sunchrom Sprayer.
Sample preparation and cryosectioning
Remove fresh frozen tissue sample stored at -80°C and place in cryostat at -20°C (kidney)/ -17°C (liver)/ -22°C (brain)
Mount the sample on chuck by pipetting small droplets of water and placing the sample on top until the water is frozen
Make sections of 12 µm thickness
Collect the sections on an ITO slide (for MALDI-MSI) or a glass slide (for H&E staining) and thaw mount the tissue onto the slide byy warming the slide with the back of your hand
Perform serial sectioning and xcollect the samples alternately on ITO and glass slides to allow for localzation and orientation of each ion image generated in MALDI-MSI to its histological counterpart
Place the slides in a slide holder and store at -80°C
Matrix application
Dry the sample in a vaccuum dessiccator at -0.1 MPa until dry (20-25 min)
Prepare N-(1-naphtyl)ethylenediamine hydrochloride (NEDC) at a concentration of 7 mg/mL in MeOH:ACN:H2O (70:25:5)
Turn on sprayer, pump (35 psi) and the connected computer
Take 250 µL syringe, fill it with MeOH and rinse the lines of the sprayer manually
Open the Suncollect software and enter the sprayer settings and coordinates of your tissue (based on the size of your sample)
Screenshot of the SunCollect software
Screenshot of the commands in the SunCollect software
Screenshot of the software parameters and tissue coordinates in the suncollect software
Sprayer setting:
| A | B | |
| Vial Distance in X | 0.50 mm | |
| Vial distance in Y | 2.00 mm | |
| Z Position | 35.00 mm | |
| Z Offset | 25.00 mm | |
| Speed X | Low, 8 | |
| Speed Y | Medium 1 |
Method parameters for the SunChrom sprayer
Fill the syringe with the prepared NEDC (solution (overfill), remove airbubbles and connect the syringe to the dispenser
Manually press the syringe until you have removed remaining airbubbles in the lines (the spray will stop shortly if there's an airbubble)
Place your tissue
In the suncollect software select your syringe size and set it to filled
Screenshot of the commands in the SunCollect Software
Screenshot of the refill syringe command
Prepare your sprayer method. For this protocol you will need four separate methods (Layer 1-3, Layer 4-6, Layer 7-9 and Layer 10-21).
Screenshot of the flow rate method for layer 1-3. In total 4 methods are needed
Sprayer method
| A | B | |
| Layer 1-3 | 5 µL/mL | |
| Layer 4-6 | 10 µL/mL | |
| Layer 7-9 | 15 µL/mL | |
| Layer 10-21 | 20 µL/mL |
Flowrate for the different layers of the NEDC method
Start the spraying method. While spraying, watch the syringe and refill inbetween the layers if empty. While refilling, also set the syringe status to filled again in the software
Screenshot of the commands in the Suncollect Software
After spraying, remove the tissue
Clean you sample holder and fill the syringe again with MeOH to manually clean the lines
Consumables
| A | B | |
| Cryostat | Cm 1860, Leica, Nußloch, Germany | |
| Blades | DB80 LX Low Profile Microtome Blades, Leica, Nußloch, Germany | |
| ITO-slides | Part No. CG-90IN-S115, Delta Technologies, Loveland, USA | |
| Glass slides | Micro Slides 2948-75X25, Corning Incorporated, NY, USA | |
| N-(1-naphtyl)ethylenediamine hydrochloride | CAS: 1465-25-4, PCode: 1003246811, Merck, St Louis, USA | |
| Sprayer | SunChrom Micro Fraction Collector MALDI Spotter Suncollect | |
| Sprayer software | SunCollect Version 1.7.43 |
Used consumables and instruments
Protocol references
Wang, G., Heijs, B., Kostidis, S. et al. Analyzing cell-type-specific dynamics of metabolism in kidney repair.
Nat Metab 4, 1109–1118 (2022). https://doi.org/10.1038/s42255-022-00615-8
Zhou Q, Fülöp A, Hopf C. Recent developments of novel matrices and on-tissue chemical derivatization reagents for MALDI-MSI. Anal Bioanal Chem. 2021 Apr;413(10):2599-2617. doi: 10.1007/s00216-020-03023-7. Epub 2020 Nov 19. PMID: 33215311; PMCID: PMC8007514.