May 06, 2025
Staining protocol for Imaging Mass Cytometry
- Vijayakumar R Kakade1,
- Tifanny Budiman1,
- Lloyd Cantley1
- 1Yale University School of Medicine
- KPMPTech. support email: info@kpmp.org
Protocol Citation: Vijayakumar R Kakade, Tifanny Budiman, Lloyd Cantley 2025. Staining protocol for Imaging Mass Cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6ywn5vqe/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: May 06, 2025
Last Modified: May 06, 2025
Protocol Integer ID: 217796
Funders Acknowledgements:
NIDDK
Grant ID: U01DK133768
Abstract
In Imaging Mass Cytometry (IMC), a high-resolution laser is combined with a mass cytometer that permits mass spectrometry-based, spatially reserved high-dimensional analysis of intact formalin-fixed paraffin-embedded (FFPE) tissues. The protocol summarizes the staining procedure for IMC using a cocktail of heavy metal conjugated primary antibodies identifying specific antigens.
Guidelines
Protocol Quality Control metrics
- Antibody validation: All primary antibodies included in the panel are validated either by the vendor or internal validation. Strategies considered for antibody validation include: 1) knockout/knockdown of gene of interest, 2) independent antibody verification, 3) morphological validation by performing IF using single common protocol on human kidney and positive control tissue (lymph node, tumors etc), 4) morphological validation by a renal pathologist blinded to the antibody used and 5) counterstaining for additional markers of the same cell type.
- Aperio scanned image of PAS-stained section of the entire biopsy is evaluated for tissue morphology and integrity.
- Use 5 µm thick sections for staining. For better results, stain and ablate the tissue within 2 weeks of sectioning.
- Entire biopsy is ablated with increments in approximately 3 mm2 area to complete ablation of the cortical and medullary regions. Regions with artifactual section damage are excluded.
- Each IMC analysis includes a section from a reference kidney, both cortex and medulla (quality control), on the same slide as an internal standard.
- IMC is performed on the Hyperion XTi imaging system. Prior to ablation of tissue, the machine undergoes routine tuning and calibration for mass spectrometric detection of all the heavy metals used in the antibody panel each time.
- For each IMC ablation, the steps of antigen retrieval and cocktail hybridization will be confirmed by visual inspection of the resident cell type markers using mcd viewer to identify the nuclei, proximal tubules, glomeruli, thick ascending limb, distal convoluted tubules and collecting duct to confirm that the correct region was ablated and analyzed.
Materials
Xylenes - JT Baker (9490-05)
Ethanol – Decon Labs (2805M)
10X Phosphate buffered saline (PBS) - Gibco (70011044)
10X Tris buffered saline (TBS) - BioRad (1706435)
Triton X-100 - Sigma (X100RS-5G)
Epitope Retrieval Reagent pH 9 (10x) - Leica Biosystems (RE7113-CE)
Bovine serum albumin (BSA) - American Bio (AB0048)
Double distilled water
PAP pen - Abcam (ab2160)
Maxpar IMC Cell Segmentation - Standard Biotools (201500)
Intercalator-Ir - Standard Biotools (201192A)
Antibodies (as listed on Table 1)
Before start
| Type | Target | Cell Type | Species | Vendor (Cat No.) | Dilution | Metal Conjugate | |
| Resident Cell Panel | Beta catenin | Tubular epithelium | Mouse | Standard Biotools (3147005A) | 1:500 | 147Sm | |
| Aqp1 | Proximal tubule | Rabbit | Abcam (ab178352-1001) | 1:2500 | 173Yb | ||
| Megalin | Proximal tubule | Mouse | Millipore (MABS489) | 1:250 | 174Yb | ||
| Uromodulin | Thick ascending limb | Rat | R&D Systems (MAB5175) | 1:1600 | 151Eu | ||
| Calbindin | Distal convoluted tubule | Mouse | ThermoFischer (MA524135) | 1:400 | 142Nd | ||
| CK7 | Collecting duct | Mouse | Standard BIotools (3164028D) | 1:150 | 164Dy | ||
| Nestin | Podocytes | Mouse | Abcam (ab6320-1001) | 1:200 | 146Nd | ||
| Vimentin | Fibroblasts, pericytes, podocytes | Mouse | Abcam (ab8978-1001) | 1:400 | 150Nd | ||
| CD31 | Endothelium | Mouse | Abcam (ab212712-1001) | 1:100 | 149Sm | ||
| ERG | Endothelium | Rabbit | Abcam (ab214796-1001) | 1:500 | 166Er | ||
| alpha-SMA | Smooth muscle, mesengial | Mouse | Standard Biotools (3141017D) | 1:1000 | 141Pr | ||
| WT1 | Podocytes | Mouse | ThermoFischer (MA146028) | 1:100 | 176Yb | ||
| Aqp2 | Collecting duct | Rabbit | Abcam (ab230170) | 1:200 | 154Sm | ||
| Immune Cell Panel | CD68 | Macrophages | Mouse | Fluidigm (3159035D) | 1:800 | 159Tb | |
| CD14 | Pro-Inflammatory Macrophages (M1) | Rabbit | Fluidigm (3144025D) | 1:100 | 144Nd | ||
| CD163 | Alternative Activated Macrophages (M2) | Mouse | Bio-Rad (MCA1853) | 1:100 | 148Nd | ||
| CD206 | Alternative Activated Macrophages (M2) | Rabbit | Abcam (AB64693) | 1:400 | 163Dy | ||
| CD11c | Dendritic cell | Rabbit | Abcam (AB216655) | 1:200 | 167Er | ||
| CD3 | T cell | Mouse | Novus Biologicals (NBP2-54392-100) | 1:250 | 170Er | ||
| CD4 | Helper T cells | Rabbit | Fluidigm (3156033D) | 1:100 | 156Gd | ||
| CD8a | Cytotoxic T cells | Mouse | Fluidigm (3162034D) | 1:300 | 162Dy | ||
| CD20 | B cells | Mouse | Fluidigm (3161029D) | 1:150 | 161Dy | ||
| MBP | Eosinophils | Mouse | Novus Biologicals (NBP1-42140-MTO) | 1:20 | 143Nd | ||
| MPO | Neutrophils | Rabbit | Abcam (AB236022) | 1:500 | 172Yb | ||
| Chymase | Mast cells | Rabbit | Abcam (AB233729) | 1:400 | 165Ho | ||
| CD56 | NK cells | Mouse | Cell Signaling (97174SF) | 1:200 | 175Lu | ||
| Injury Cell Panel | Kim1 | Epithelial injury/repair | Mouse | R&D Systems (MAB1750-100) | 1:300 | 160Gd | |
| Ki67 | Proliferation | Mouse | Fluidigm (3168022D) | 1:100 | 168Er | ||
| IL9 | Cytokine | Rabbit | Abcam (ab181397) | 1:250 | 153Eu | ||
| FACL4 | Ferroptosis | Rabbit | Abcam (ab240135) | 1:400 | 155Gd | ||
| MCP-1 | Cytokine | Mouse | Novus Biologicals (NBP2-22115) | 1:300 | 169Tm | ||
| TNFa | Cytokine | Rabbit | Abcam (ab271989) | 1:300 | 145Nd | ||
| LC3b | Autophagy | Rabbit | Abcam (ab221794-1001) | 1:200 | 158Gd | ||
| VCAM-1 | Epithelial injury/repait | Rabbit | Abcam (ab271899-1001) | 1:200 | 152Sm | ||
| Segmentation Kit | ICSK1 | Membrane | - | Standard Biotools (201500) | 1:400 | 195Pt | |
| ICSK2 | Membrane | - | Standard Biotools (201500) | 1:400 | 196Pt | ||
| Intercalator | DNA | - | Standard Biotools (201192A) | 1:1000 | 191Ir/193Ir |
Table 1. Antibody Panel
Staining Tissue Sections
Staining Tissue Sections
4h 20m
4h 20m
Bake the slides Overnight at 60°C. Ensure that all visible wax has been removed
Dewax the slides in xylenes in the fume hood for 00:10:00
10m
Repeat step 2 and dewax the slides in fresh xylene in the fume hood for 00:10:00
10m
Hydrate the slides in descending grades of ethanol (100%, 95%, 80%, 70%) for 00:05:00 each.
5m
Wash the slides in double distilled water for 00:05:00 in a Coplin jar placed on an orbital shaker plate with gentile agitation.
5m
Perform antigen retrieval bu immersing slides in 1X epitope retrieval bugger (pH 9.0) for 00:20:00 in a steamer
20m
Prepare 1X epitope retrieval buffer from its 10X stock solution.
Cool slides for 00:40:00
40m
Wash the slides in double distilled water for 00:05:00 in a Coplin jar with gentle agitation on an orbital shaker. Perform this step twice.
5m
Wash the slides with 1X TBS for 00:10:00 with gentle agitation on an orbital shaker.
10m
Use a PAP pen to draw an outline encircling the sample.
Block with 3% BSA in 1X TBS for 01:00:00 at room temperature in a hydration chamber.
1h
You can use an empty pipette tip box where the slides rest on the tip shelf and the bottom is filled halfway with water.
Blocking solution should be diluted from 10% BSA freshly made from powder. The remaining 10% BSA should be aliquoted and stored at -20°C and diluted at time of use.
Use enough blocking solution to cover the section.
Prepare the antibody cocktail calculating the total volume of antibodies at the concentrations specific for the assay and bring the volume up to a final volume using 0.5% BSA. in 1X TBS.
Dilutions can be found on Table 1.
Place the slides in a hydration chamber and pipette the antibody mix on to the section.
Store the antibody cocktail mix on ice and add it on to the samples within 1-2 hours of preparation for best results.
Incubate overnight with the antibody cocktail at 4°C in a hydration chamber.
Wash the slides in 0.1% Triton X-100 in 1X TBS for 00:05:00 in Coplin jars with slow agitation on an orbital shaker.
5m
Repeat step 15 two more times.
Wash the slides in 1X TBS for 00:05:00 with gentle agitation on an orbital shaker.
5m
Repeat step 17.
Stain the tissue with Intercalator-Ir in 1X PBS (1:1000) for 01:00:00 at room temperature in a hydration chamber.
1h
Wash the slides in double distilled water for 00:05:00 with gentle agitation on an orbital shaker.
5m
Air dry the slides for at least 00:20:00 at room temperature.
20m
Imaging Mass Cytometry
Imaging Mass Cytometry
Load the stained slide into the pre-tuned and pre-calibrated Hyperion XTi IMC System.
Create a new project on the CyTOF software.
Draw a panorama that covers the tissue that will be ablated.
Determine regions of interest (ROIs) to ablate with increments less than 3mm2 on the tissue, ensuring that cortical and medullary regions are separate within the panorama created. Regions with artificial section damage are excluded.
Create or select an antibody/metal template.
Make sure to select "generate txt file".
Save the project file and start ablation of tissue.
Image Verification
Image Verification
Once ablation is complete, load the file on MCD viewer to check the quality of each image and channel.