Feb 09, 2023

Public workspaceHuBMAP | GE/Vanderbilt MALDI IMS and Cell DIVE™ Modality Overview

DOI
dx.doi.org/10.17504/protocols.io.kqdg39k41g25/v1
  • 1Vanderbilt University;
  • 2UC Davis;
  • 3GE Research
Liz McDonough
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DOI: dx.doi.org/10.17504/protocols.io.kqdg39k41g25/v1
Protocol Citation: Nathan Heath Patterson, Elizabeth Neumann, Christine Surrette, Soumya Ghose, Liz McDonough, Jamie Allen, Jeff Spraggins, Fiona Ginty 2023. HuBMAP | GE/Vanderbilt MALDI IMS and Cell DIVE™ Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.kqdg39k41g25/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: December 21, 2022
Last Modified: February 09, 2023
Protocol Integer ID: 74344
Funders Acknowledgement:
HuBMAP (Vanderbilt University)
Grant ID: U54DK134302
HuBMAP (GE Research)
Grant ID: 5UH3CA246594-02
Abstract
This is an overview of all protocols currently in use for the GE/Vanderbilt University Cell DIVE collaboration for the Human BioMolecular Atlas Program (HuBMAP). It includes links to each of the individual protocols that make up this project workflow.
MALDI IMS
MALDI IMS
Collection of post-surgical tissue.
Protocol
Collection and Post-Surgical Excision of Human Kidney Tissue through the Cooperative Human Tissue Network
NAME

Collection and Post-Surgical Excision of Human Kidney Tissue through the Cooperative Human Tissue Network

CREATED BY
Jamie Allen

Stabilize and freeze tissues.
Protocol
Freezing Fresh Tissue
NAME

Freezing Fresh Tissue

CREATED BY
Jamie Allen

Cryosection tissues into micrometer thick sections, alternating between thaw mounting onto indium tin-oxide and positively charged glass slides (proceed to step 4), or collecting several tissue sections within an microcentrifuge tube for proteomics analysis.
Protocol
Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging
NAME

Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging

CREATED BY
Jamie Allen

Perform autofluorescence microscopy on all tissue sections
Protocol
Autofluorescence Microscopy Data Acquisition
NAME

Autofluorescence Microscopy Data Acquisition

CREATED BY
Jamie Allen

Perform Matrix Application

Protocol
Automatic Deposition of CHCA Matrix for MALDI Analysis of Lipids
NAME
Automatic Deposition of CHCA Matrix for MALDI Analysis of Lipids
CREATED BY
Jamie Allen


Perform high resolution IMS analysis of matrix coated tissue sections.
Protocol
High Resolution Imaging Mass Spectrometry Analysis using Bruker Daltonics Platforms
NAME

High Resolution Imaging Mass Spectrometry Analysis using Bruker Daltonics Platforms

CREATED BY
Jamie Allen


Obtain autofluorescence microscopy images of tissues after IMS analysis

Protocol
Post-IMS Autofluorescence Microscopy
NAME

Post-IMS Autofluorescence Microscopy

CREATED BY
Jamie Allen


Preparing Sample for MxIF
Preparing Sample for MxIF
Perform Matrix Removal & Tissue Fixation

Protocol
Fixation Protocol for Fresh Frozen Tissue Samples (post-MALDI)
NAME
Fixation Protocol for Fresh Frozen Tissue Samples (post-MALDI)
CREATED BY
Jamie Allen

Cell DIVE
Cell DIVE
Characterize antibodies (primary/secondary, direct conjugates, and zenon labelled antibodies) and determine any antigen effects from the Cell DIVE dye inactivation process.


Cell DIVE™ Platform | Antibody Characterization for Multiplexing
Cell DIVE™ Platform | Antibody Staining & Imaging

Perform Cell DIVE™ multiplexed data acquisition on the final cohort.

Note
Staining is done manually using a humidity chamber and images are acquired on the Leica Cell DIVE imager utilizing a coverslipless imaging approach