Jun 14, 2026
Preparation of Lung Tissue Blocks for MPLEx
- 1Pacific Northwest National Lab;
- 2Pacific Northwest National Laboratory
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: [email protected]
Protocol Citation: Brittney Gorman, Christopher Anderton, Geremy Clair 2026. Preparation of Lung Tissue Blocks for MPLEx . protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlk1myxg5r/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: January 29, 2026
Last Modified: June 14, 2026
Protocol Integer ID: 241749
Keywords: preparation of lung tissue block, lung tissue block, protocol for mass spectrometry analysis, embedded lung tissue, mass spectrometry analysis, mplex, lung tissue, protein extraction, metabolite, lipid
Funders Acknowledgements:
The Human Lung BioMolecular Multi-Scale Atlas Program (HuBMAP-Lung)
Grant ID: U54HL165443
Biorepository for Investigation of Neonatal Diseases of Lung-Normal (BRINDL-NL)
Grant ID: U01HL122700
Biorepository for INvestigation of Diseases of the Lung (BRINDL) - Phase II
Grant ID: U01HL148861
Abstract
This protocol details how CMC- and OCT-embedded lung tissue were handled before being submitted to the Metabolites, Lipids, and Protein Extraction (MPLEx) protocol for mass spectrometry analysis.
Guidelines
Always wear appropriate PPE.
Cryosectioning requires safety glasses, gloves, and a lab coat
Materials
Cryostat (Thermo Fisher CryoStar NX70)
Protocol materials
2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVWR International (Avantor)Catalog #53550
Rapid-Core Sampling Punch - 4 mmTed Pella Inc.Catalog #15115-10
Safety warnings
Biosafety Level II precautions should be in place BSL-2 controls should be used for Human tissue samples
Ethics statement
The protocols.io team notes that research involving animals and humans must be conducted according to internationally-accepted standards and should always have prior approval from an Institutional Ethics Committee or Board.
Before start
Label and weigh a 2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVWR International (Avantor)Catalog #53550 for each sample.
Fresh-Frozen non-embedded Tissue
Place the sample in the cryostat (allow to thermally equilibrate ~20 min)
Set blade temperature -16 °C and specimen temperature of -14 °C
Cut 2x sections (50 μm) and place sections in pre-weighed 2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVWR International (Avantor)Catalog #53550
OCT-embedded Tissue
Place the sample in the cryostat (allow to thermally equilibrate ~30 min)
Set blade temperature -18 °C and specimen temperature of -16 °C
Cut 2x sections (50 μm)
Use a Rapid-Core Sampling Punch - 4 mmTed Pella Inc.Catalog #15115-10 to punch 2 tissue cores from each tissue section and place the punches in pre-weighed 2 mL Sorenson MµlTI™ SafeSeal™ Microcentrifuge TubesVWR International (Avantor)Catalog #53550
*Note: When punching the tissue cores, avoid regions with OCT, as this can be difficult to remove from the sample and may yield contamination within the mass spectrum.
Two 50 μm tissue sections after punching two 4 mm tissue cores
Storage
Acknowledgements
This work was supported by the National Heart, Lung, and Blood Institute (NHLBI) Molecular Atlas of Lung Development Program Human Tissue Core (LungMAP HTC) and LungMAP BioRepository for INvestigation of Diseases of the Lung (BRINDL) through grants U01HL122700 and U01HL148861 (to GSP), and U01HL148860 (G. Clair) and by the NIH Common Fund grant U54 HL165443-01 (to GSP, with Co-Investigators GC, and CA). Part of this work was performed in the Environmental Molecular Science Laboratory, a U.S. Department of Energy (DOE) national scientific user facility at Pacific Northwest National Laboratory (PNNL). Battelle operates PNNL for the DOE under contract DE-AC05-76RLO01830. The opinions expressed in this article are the authors’ own and do not reflect the view of the NIH, the Department of Health and Human Services, or the U.S. government. We are very grateful for the generosity of the donor families and honor their loss.