Apr 07, 2025
Version 2
Tissue Preparation for Spatial Metabolomics V.2
- Guanshi Zhang1,
- Brittney Gorman2,
- Leila Hejazi1,
- Dusan Velickovic2,
- Theodore Alexandrov3,
- Christopher R Anderton2,
- Kumar Sharma1
- 1University of Texas Health San Antonio;
- 2Pacific Northwest National Laboratory;
- 3European Molecular Biology Laboratory
- KPMPTech. support email: info@kpmp.org
Protocol Citation: Guanshi Zhang, Brittney Gorman, Leila Hejazi, Dusan Velickovic, Theodore Alexandrov, Christopher R Anderton, Kumar Sharma 2025. Tissue Preparation for Spatial Metabolomics. protocols.io https://dx.doi.org/10.17504/protocols.io.d7gf9jtnVersion created by Guanshi Zhang
Manuscript citation:
Nakayasu et al., 2016. MPLEx: a robust and universal protocol for single-sample integrative proteomic, metabolomic, and lipidomic analyses. mSystems 1(3):e00043-16.
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: February 20, 2020
Last Modified: April 07, 2025
Protocol Integer ID: 126183
Abstract
Mass spectrometry imaging (MSI) is a cutting-edge molecular technology that enables simultaneous analysis of multiple molecular components directly from single cells, tissues, and organs. For MSI, cryosections are prepared from flash-frozen tissue and mounted on a contuctive glass slide. We use matrix-assisted laser desorption ionization (MALDI)-MSI, where tissue sections are coated with a MALDI matrix in order to facilitate laser ionization and detection of metabolites with mass spectrometry. We do it using an automated robotic sprayer (TM-Sprayer) with 2,5- dihydroxybenzoic acid (DHB) MALDI matrix for positive ion mode analysis, N-(1-naphthyl) ethylenediamine hydrochloride (NEDC) for negative ion mode analyses, or 1,5-Diaminonaphthalene (DAN) for dual-polarity analysis, prior to being loaded into the MALDI-Q Exactive HF-X Orbitrap-MSI or MALDI-FTICR-MSI for untargeted metabolomics analysis. We have optimized a method for matrix application to maximize analyte extraction from tissue and increase MALDI sensitivity and to create the most homogenous matrix films possible for best lateral resolution of lipids. A key capacity that will be critical for scale-up in KPMP is the use of a TM-sprayer robotic sprayer for MALDI matrix application. This will make inter-lab studies viable, by increasing the reproducibility of sample preparation and is currently in use at UTHSA and PNNL. Our lipid extraction protocol for LC-MS/MS is a robust and universal protocol for single-sample integrative proteomics, metabolomics, and lipidomics analyses (see citation).
Guidelines
Key characteristics of TM-Sprayer robotic sprayer for MALDI-specific tissue preparation
1. Patented technology providing very small matrix droplets (<20 microns)
2. High flow rate and fast sample prep (10 to 20 minutes per plate)
3. Highly consistent matrix deposition across entire sample area (+/- 3% by weight)
4. Unique use of temperature and nitrogen flow to control evaporation rate and matrix crystal formation
5. Validated protocols for most matrices (e.g.: DHB, DAN, NEDC)
6. Continuous matrix coverage as needed for high-resolution imaging
7. Rugged operation and easy clean-up
Data types and file formats
Data generated from MS imaging is in the format of either a .d/.mis or .raw (Bruker- and Thermo-based instruments, respectively). These files are converted to the universal MSI file format (.imzML/.ibd) for further data processing and metabolite annotations in SCiLS and METASPACE.
Quality Control
As quality control, in all MALDI imaging optimization, the number of ions annotated by METASPACE (https://metaspace2020.eu/) at 20% false discovery rate (FDR) was used as the main benchmark. All experiments are performed at least in duplicates and results are presented accordingly.
Materials
MATERIALS
Dry ice
Parafilm™ M Laboratory Wrapping Film, 4 in. W x 125 ft. L; (10cm x 38m)Thermo FisherCatalog #1337410
CryoStar NX50 Cryostat with height adjustment, Vacutome, Cold D, 100VThermo FisherCatalog #957090
CM1950 CryostatLeica Biosystems
Tissue-Tek Accu-Edge Disposable Microtome BladesSakura FinetekCatalog #4689
Conductive ITO Coating Glass Slides for MALDI ImagingBrukerCatalog #8237001
Superfrost Plus Microscope SlidesFischer ScientificCatalog #12-550-15
4 x 6 Zipper Bag
Pocket Scriber Carbide w/Magnet EndCatalog #Westward #4KY32
Flatbed Scanner
MTP Slide-Adapter IIBrukerCatalog #8235380
Tissue MALDI TM-SprayerHTX Technologies, LLC
25-Dihydroxybenzoic acid (DHB >98%)Sigma Aldrich
15-Diaminonaphthalene (DAN 99%)Sigma Aldrich
Chloroform (HPLC grade)Sigma Aldrich
Methanol (HPLC grade)Sigma Aldrich
Water (miliQ)
Acetone (HPLC grade)Sigma Aldrich
Ethanol (HPLC grade)Sigma Aldrich
Hydrogen chloride solution (HCl 1M)Sigma Aldrich
Vacuum Desiccator
FastPrep-24 HomogenizerMP BiomedicalsCatalog #116004500
Balance (500 mg)
Container to hold dry ice
Weigh boat
Spatula
Falcon 50mL Conical Centrifuge TubesFisher ScientificCatalog #14-432-22
Metal Bead Lysing MatrixMP BiomedicalsCatalog #6925050
Wild type adult mouse kidneys (avg 200mg/kidney 12 kidneys >2g total)
Sphingomyelin (d18:1/16:0)Cayman Chemical CompanyCatalog #10007946
13C Sphingomyelin 1:(d18:1/16:0)Cayman Chemical CompanyCatalog #24452
Centrifuge
Pipette and tips (20 - 300 µL)
2 mL screw cap vials (1 per layer of the mimetic model)
Water (deionized)
3 mL SyringeBdCatalog #309657
Beaker
Dry ice-cooled ethanol
Ammonium Acetate (HPLC grade)Sigma Aldrich
Acetonitrile (HPLC grade)Sigma Aldrich
Isopropyl alcohol (HPLC grade)Sigma Aldrich
2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVwrCatalog #53550
Waters autosampler vial
NEDC (N-(1-naphthyl) ethylenediamine hydrochloride)
STEP MATERIALS
2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVwrCatalog #53550
Methanol (HPLC grade)Sigma Aldrich
Chloroform (HPLC grade)Sigma Aldrich
Chloroform (HPLC grade)Sigma Aldrich
Methanol (HPLC grade)Sigma Aldrich
Chloroform (HPLC grade)Sigma Aldrich
Methanol (HPLC grade)Sigma Aldrich
Tissue MALDI TM-SprayerHTX Technologies, LLC
4 x 6 Zipper Bag
MTP Slide-Adapter IIBrukerCatalog #8235380
Flatbed Scanner
Tissue-Tek Accu-Edge Disposable Microtome BladesSakura FinetekCatalog #4689
Conductive ITO Coating Glass Slides for MALDI ImagingBrukerCatalog #8237001
Superfrost Plus Microscope SlidesFischer ScientificCatalog #12-550-15
Pocket Scriber Carbide w/Magnet EndCatalog #Westward #4KY32
Conductive ITO Coating Glass Slides for MALDI ImagingBrukerCatalog #8237001
Protocol materials
Tissue MALDI TM-SprayerHTX Technologies, LLC
Step 9
Conductive ITO Coating Glass Slides for MALDI ImagingBrukerCatalog #8237001
In 2 steps
Chloroform (HPLC grade)Merck MilliporeSigma (Sigma-Aldrich)
In 3 steps
Tissue-Tek Accu-Edge Disposable Microtome BladesSakura FinetekCatalog #4689
Step 2
Superfrost Plus Microscope SlidesFischer ScientificCatalog #12-550-15
Step 3
Pocket Scriber Carbide w/Magnet EndCatalog #Westward #4KY32
Step 3
4 x 6 Zipper Bag
Step 5
Flatbed Scanner
Step 8
Methanol (HPLC grade)Merck MilliporeSigma (Sigma-Aldrich)
In 3 steps
MTP Slide-Adapter IIBrukerCatalog #8235380
Step 8
2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVWR International (Avantor)Catalog #53550
Step 38
Snap frozen (liquid N2) sample preparation and sectioning
Snap frozen (liquid N2) sample preparation and sectioning
Remove fresh frozen (liquid nitrogen) kidney sample stored at -80 °C and place in cryostat set at -15 °C
Mount the sample on chuck with minimal amount of water (one droplet) and make 7 µm sections, while keeping chuck temperature at -15 °C and blade temperature at -20 °C .
Tissue-Tek Accu-Edge Disposable Microtome BladesVWR InternationalCatalog #4689
Thaw-mount in sequential order as outlined in Figure 1. Dry the sections immediately after sectioning in the cryostat chamber. Each slide will be marked with a number via a scribe.
Figure 1. Sandwich model of human kidney biopsy tissue
Conductive ITO Coating Glass Slides for MALDI ImagingVWR InternationalCatalog #8237001
Superfrost Plus Microscope SlidesVWR InternationalCatalog #12-550-15
Pocket Scriber Carbide w/Magnet EndVWR InternationalCatalog #Westward #4KY32
Tissues will be cut to generate adjacent slides that are alternatively subjected to histological staining or MALDI-MSI. This sandwich like assignment allows proper orientation and localization of each MALDI-MSI ion image to its histological counterpart.
ITO slides with mounted coss-sections are then transferred directly from the cryostat to either the vacuum desiccator OR zipper bag.
4 x 6 Zipper BagVWR International
For imaging later: Place ITO slides in a zipper bag to keep vacuum inside of the bag for storing in the -80 °C freezer (sectioned samples can be stored in the freezer for months but should be analyzed as soon as possible). When removing the bag from the freezer, keep it close for ~5 minutes to reach RT before opening it.
For immediate imaging: Place ITO slides in the vacuum desiccator at Room temperature for drying 00:20:00
Regular glass slides are stored at -80 °C untiil staining
All slides (regular and ITO) stored at -80 °C are placed in the vacuum desiccator to defrost
For the 15T Fourier Transform Ion Cyclotron Resonance (FTICR) Mass Spectrometry, MALDI imaging slides are mounted in the Bruker MTP Slide Adapter II and scanned with a flatbed scanner with at least 3200 dpi resolution (output JPEG, TIFF, or PNG).
Note
This is performed so that the optical image can be co-registered with the imaging experiment run. Visible fiducials (e.g., "X" marks) are previously placed onto MTP Slide Adapter to use as teaching points to register the optical and MS images.
MTP Slide-Adapter IIVWR InternationalCatalog #8235380
Flatbed ScannerVWR International
Visible fiducials (e.g., "X" marks) are previously placed onto MTP Slide Adapter to use as teaching points to register the optical and MS images.
Matrix application for MALDI-MSI: Start-up
Matrix application for MALDI-MSI: Start-up
Turn on TM-Sprayer unit. Set valve to LOAD position.
Tissue MALDI TM-SprayerVWR International
Launch TM-Sprayer Software
Note
IMPORTANT: Check that exhaust fan is operational. Do not start solvent pump if proper active venting is not functioning.
Start solvent pump at 0.100 mL/min. Backpressure should be normal. ~ 500 psi (3.4 MPa)
Start compressed air flow to TM-Sprayer. Set at 10 psi (70 kPA).
Adjust operating temperature on the sprayer device per solvent mixture.
Note
Follow safety instructions. SOLVENT MIXTURE SHOULD CONTAIN 30% WATER MINIMUM.
Prepare matrix solution. Typical concentration is 5 Mass Percent
Note
Positive ion mode:
DHB is used at 40 Mass Percent in 1:1 MeOH:Water; 80 °C ; 3mm/track spacing; 8 cycles; 1200 mm/min spraying velocity; 0.05 mL/min matrix flow
25-Dihydroxybenzoic acid (DHB >98%)Sigma Aldrich
DAN is used at 4.4 Mass Percent in 9 mL of 1:1 Ethanol:Water (Add 500 µL of 1M HCl in 4 mL milli'Q' water and 4.5 mL of ethanol); 90 °C ; 3 mm/track spacing; 16 cycles; 1250 mm/min spraying velocity; 0.05 mL/min matrix flow
15-Diaminonaphthalene (DAN 99%)Sigma Aldrich
Note
Negative ion mode
NEDC is used at 7 Mass Percent in 7:3 Methanol:Water; 70 °C ; 3 mm/track spacing; 8 passes; 1200 mm/min spraying velocity; 0.12 mL/min matrix flow
NEDC (N-(1-naphthyl) ethylenediamine hydrochloride)
DAN is used at 4.4 Mass Percent in 9 mL of 1:1 Ethanol:Water (Add 500 µL of 1M HCl in 4 mL milli'Q' water and 4.5 mL of ethanol); 90 °C ; 3 mm/track spacing; 16 cycles; 1250 mm/min spraying velocity; 0.05 mL/min matrix flow.
15-Diaminonaphthalene (DAN 99%)Sigma Aldrich
NOTE: These are, for now, the optimal condition for matric spraying based on METASPACE output and spatial resolution achieved, and we will continue to optimize both matrix applications.
With valve in LOAD position, use a syringe to fill loop with matrix.
Note
20% overfill is recommended (e.g. Use 6 mL syringe to fill 5 mL loop)
Matrix application for MALDI-MSI: Sample preparation
Matrix application for MALDI-MSI: Sample preparation
Bring ITO glass slide with affixed sample(s) from dessicator.
Conductive ITO Coating Glass Slides for MALDI ImagingVWR InternationalCatalog #8237001
Check that the flow rate of the solvent pump and temperature of the spray nozzle are correct and stable.
Review sample position and define spraying area in TM-Sprayer software.
Select Method by clicking on left column. Current Method field will confirm selection.
Press START. Option changes to CONTINUE. Follow STATUS tab for prompts.
When prompted, switch valve to Spray and confirm by clicking Continue.
Software will automatically delay start to allow purging of liquid lines.
At end of the run the spray nozzle automatically goes to Waste position.
Follow end of run prompts. Software will keep track of usage and remaining matrix volume.
Matrix application for MALDI-MSI: Pause Mode
Matrix application for MALDI-MSI: Pause Mode
At the end of sample prep sequence, swith the valve back to LOAD.
Note
IMPORTANT: Keep solvent pump flow on so that clean solvent flows to nozzle and prevents matrix residues from crystallizing and clogging the capillary and spray nozzle.
Spray at 0.200 mL/min for 00:10:00 , then at 0.010 mL/min until ready to resume.
To resume, start at step 16.
Matrix application for MALDI-MSI: Shut down
Matrix application for MALDI-MSI: Shut down
Switch valve back to LOAD position. Set solvent pump flow rate at 0.500 mL/min.
Set Temperature to 30 °C to start cool down.
Fill syringe with 5 mL to 6 mL of clean solvent and flush loop completely. Repeat 3 times.
Toggle valve to wash matrix residue. Leave valve in LOAD position.
Keep airflow and solvent pump flow on until temperature is below 50 °C .
Note
This is important to prevent clogging.
Turn N2 flow off (droplet will form at nozzle tip).
Stop solvent pump flow.
Exit TMSP Software.
Power OFF TM-Sprayer. Power OFF solvent pump.
Lipid extraction for LC-MS/MS
Lipid extraction for LC-MS/MS
Add MilliQ water (200 µL to 300 µL ) to the biopsy tube containing the remaining fresh frozen (liquid N2) biopsy sample (i.e. not sectioned) and lyse the remaining biopsy sample using a tissue lyser. Quantify the amount of tissue remaining by weight.
Place the sample into a 2 mL microcentrifuge tube.
2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVWR InternationalCatalog #53550
Note
It's been shown these tubes do not leach polymers into the lipid layer from the chloroform.
Add cold (-20 °C ) chloroform:methanol mix (prepared 2:1 v/v) to sample in 4:1 ratio over sample volume and vortex.
Methanol (HPLC grade)VWR International
Chloroform (HPLC grade)VWR International
Note
i.e. add 400 μl of the 2:1 chloroform:methanol mixture to 80 μl of sample
Vortex for 00:00:05 to 00:00:10
Let stand on ice for 00:05:00
Vortex for 00:00:05 to 00:00:10
Centrifuge the sample 12000 x g, 4°C, 00:10:00 , 5-10 min
Carefully remove the upper aqueous metabolite layer until the interphase contracts without disturbing the protein disk, and discard.
Carefully puncture the protein interphase with a pipette tip, remove the organic lipid phase from the bottom of the tube into a conical bottom Waters autosampler vial.
Note
Be sure to gently push out any protein or upper methanol phase that might have entered the pipette tip.
The organic layer (containing lipids) is placed into the speed vac to dry.
500 µL of 2:1 Chl:MeOH and cap (no septa) is stored at -70 °C until ready for analysis.
Note
Requires extra solution volume for safe storage.
Chloroform (HPLC grade)VWR International
Methanol (HPLC grade)VWR International
Prior to LC analysis, dry sample in speed vac and reconsititute in 100 µL of 95:5 MeOH:Chl.
Methanol (HPLC grade)VWR International
Chloroform (HPLC grade)VWR International