Mar 06, 2026
HubMAP Lung TMC Overview of Proteomics, Lipidomics, and Metabolomics Assays From Sample Generation to Data Pre-processing
- Geremy Clair1,
- Christopher Anderton2,
- Kenichi Okuda3,
- Gloria Pryhuber4,
- Brittney Gorman1
- 1Pacific Northwest National Laboratory;
- 2Pacific Northwest National Lab;
- 3University of North Carolina at Chapel Hill;
- 4University of Rochester Medical Center
- Human BioMolecular Atlas Program (HuBMAP) Method Development Community
- Metabolomics Protocols & Workflows
Protocol Citation: Geremy Clair, Christopher Anderton, Kenichi Okuda, Gloria Pryhuber, Brittney Gorman 2026. HubMAP Lung TMC Overview of Proteomics, Lipidomics, and Metabolomics Assays From Sample Generation to Data Pre-processing. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlk1261g5r/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: February 16, 2026
Last Modified: March 06, 2026
Protocol Integer ID: 243401
Keywords: Lipidomics, proteomics, metabolomics, MPLEx, hubmap lung tmc overview of proteomic, hubmap lung tmc overview, hubmap lung tissue mapping center, metabolomics from tissue block, metabolomics assays from sample generation, metabolomics assay, proteomic, metabolomic, lipidomic, bronchus
Funders Acknowledgements:
NIH - Biorepository for Investigation of Neonatal Diseases of Lung-Normal (BRINDL-NL)
Grant ID: U01HL122700
NIH - Biorepository for INvestigation of Diseases of the Lung (BRINDL) - Phase II
Grant ID: U01HL148861
NIH - The Human Lung BioMolecular Multi-Scale Atlas Program (HuBMAP-Lung)
Grant ID: U54HL165443
NIH - Research Center for Spatiotemporal Lung Imaging and Omics
Grant ID: U01HL148860
Abstract
This master protocol summarizes the protocols utilized in the HuBMAP Lung Tissue Mapping Center (TMC) Project to generate proteomics, lipidomics, and metabolomics from tissue blocks selected from different regions of the organ from the bronchus to the alveolar and pleura regions.
Troubleshooting
Donor Tissue Block Generation
The criteria for lung inclusion in the study
The protocols for whole-lung lobe processing are provided in the following protocols.io:
Region specific tissue sampling protocol is provided in the following protocols.io:
From Blocks to Metabolites, Proteins, and Lipids
To limit block utilization and contamination by embedding material (OCT/CMC) we generated 2 50-µm-thick sections that were placed in an MPLEx compatible cryotube. The method utilized for this is provided in the following protocols.io:
From Tissue Sections to Metabolites, Proteins, and Lipids
The thick sections were further extracted using a modified Folch extraction method, termed MPLEx (Metabolites, Proteins, and Lipids), as described in the following protocols.io:
Metabolomics
After the MPLEx extraction, the metabolites were further processed using the following protocols.io:
note: this protocol comprises both the analysis method and the pre-processing of the data
Proteomics
After the MPLEx extraction, the proteins were further processed using the following protocols.io:
The prepared peptides are then injected on a dedicated liquid chromatography coupled with a tandem mass spectrometer using the following protocol:
Then the data was pre-processed using the following protocols.io:
Lipidomics
After the MPLEx extraction, the lipids were further processed using the following protocols.io:
Then the data was pre-processed using the following protocols.io:
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 GS Pryhuber), and U01HL148860 (G Clair) and by the NIH Common Fund grant U54HL165443 (to GS Pryhuber with Co-Investigators G Clair, and C Anderton). 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.