Mar 10, 2026
HubMAP Pancreas PNNL TMC Overview of Proteomics, Lipidomics, and Metabolomics Assays From Sample Generation to Data Pre-processing
- Geremy Clair1,
- Ernesto Nakayasu1,
- WEI-JUN QIAN1,2
- 1Pacific Northwest National Laboratory;
- 2HubMAP TMC-PNNL/UF
- Human BioMolecular Atlas Program (HuBMAP) Method Development Community
- Pacific Northwest National Laboratory (PNNL)
Protocol Citation: Geremy Clair, Ernesto Nakayasu, WEI-JUN QIAN 2026. HubMAP Pancreas PNNL 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.ewov1rmz7lr2/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: March 10, 2026
Last Modified: March 10, 2026
Protocol Integer ID: 313021
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, hubmap pancreas pnnl tmc overview of proteomic, hubmap pancreas pnnl tmc overview, different regions of the pancrea, pancrea, tmc
Funders Acknowledgements:
NIH - Biorepository for Investigation of Neonatal Diseases of Lung-Normal (BRINDL-NL)
Grant ID: U54DK127823
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 pancreas: head, neck, body, and tail.
Troubleshooting
From Tissue blocs 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 NIH Common Fund grant U54DK127823 (to W Qian). 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 thank the donors and families of the donors for their invaluable contribution to our research and their help to further understand and hopefully cure type 1 diabetes.