Robust collection and processing for label-free single voxel proteomics
Abstract With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures tissue heterogeneity, precluding proteome mapping of tissue microenvironment. Here we report an integ...
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| Format: | Article |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54643-x |
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| author | Reta Birhanu Kitata Marija Velickovic Zhangyang Xu Rui Zhao David Scholten Rosalie K. Chu Daniel J. Orton William B. Chrisler Tong Zhang Jeremy V. Mathews Benjamin M. Bumgarner Demirkan B. Gursel Ronald J. Moore Paul D. Piehowski Tao Liu Richard D. Smith Huiping Liu Clive H. Wasserfall Chia-Feng Tsai Tujin Shi |
| author_facet | Reta Birhanu Kitata Marija Velickovic Zhangyang Xu Rui Zhao David Scholten Rosalie K. Chu Daniel J. Orton William B. Chrisler Tong Zhang Jeremy V. Mathews Benjamin M. Bumgarner Demirkan B. Gursel Ronald J. Moore Paul D. Piehowski Tao Liu Richard D. Smith Huiping Liu Clive H. Wasserfall Chia-Feng Tsai Tujin Shi |
| author_sort | Reta Birhanu Kitata |
| collection | DOAJ |
| description | Abstract With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures tissue heterogeneity, precluding proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single microscale tissue voxels and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single voxels dissected by LCM to the tube cap and SOP voxel processing in the same collection cap. This method enables reproducible, label-free quantification of approximately 900 and 4600 proteins for single voxels at 20 µm × 20 µm × 10 µm (~1 cell region) and 200 µm × 200 µm × 10 µm (~100 cell region) from fresh frozen human spleen tissue, respectively. It can reveal spatially resolved protein signatures and region-specific signaling pathways. Furthermore, wcSOP-MS is demonstrated to be broadly applicable for OCT-embedded and FFPE human archived tissues as well as for small-scale 2D proteome mapping of tissues at high spatial resolutions. wcSOP-MS may pave the way for routine robust single voxel proteomics and spatial proteomics. |
| format | Article |
| id | doaj-art-b870c673215d44d082e68eada4faf9ff |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-b870c673215d44d082e68eada4faf9ff2025-01-19T12:31:46ZengNature PortfolioNature Communications2041-17232025-01-0116111510.1038/s41467-024-54643-xRobust collection and processing for label-free single voxel proteomicsReta Birhanu Kitata0Marija Velickovic1Zhangyang Xu2Rui Zhao3David Scholten4Rosalie K. Chu5Daniel J. Orton6William B. Chrisler7Tong Zhang8Jeremy V. Mathews9Benjamin M. Bumgarner10Demirkan B. Gursel11Ronald J. Moore12Paul D. Piehowski13Tao Liu14Richard D. Smith15Huiping Liu16Clive H. Wasserfall17Chia-Feng Tsai18Tujin Shi19Biological Sciences Division, Pacific Northwest National LaboratoryEnvironmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryBiological Sciences Division, Pacific Northwest National LaboratoryEnvironmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryDepartment of Pharmacology, Feinberg School of Medicine, Northwestern UniversityEnvironmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryBiological Sciences Division, Pacific Northwest National LaboratoryBiological Sciences Division, Pacific Northwest National LaboratoryBiological Sciences Division, Pacific Northwest National LaboratoryPathology Core Facility, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityDepartment of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of FloridaPathology Core Facility, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityBiological Sciences Division, Pacific Northwest National LaboratoryEnvironmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryBiological Sciences Division, Pacific Northwest National LaboratoryBiological Sciences Division, Pacific Northwest National LaboratoryDepartment of Pharmacology, Feinberg School of Medicine, Northwestern UniversityDepartment of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of FloridaBiological Sciences Division, Pacific Northwest National LaboratoryBiological Sciences Division, Pacific Northwest National LaboratoryAbstract With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures tissue heterogeneity, precluding proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single microscale tissue voxels and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single voxels dissected by LCM to the tube cap and SOP voxel processing in the same collection cap. This method enables reproducible, label-free quantification of approximately 900 and 4600 proteins for single voxels at 20 µm × 20 µm × 10 µm (~1 cell region) and 200 µm × 200 µm × 10 µm (~100 cell region) from fresh frozen human spleen tissue, respectively. It can reveal spatially resolved protein signatures and region-specific signaling pathways. Furthermore, wcSOP-MS is demonstrated to be broadly applicable for OCT-embedded and FFPE human archived tissues as well as for small-scale 2D proteome mapping of tissues at high spatial resolutions. wcSOP-MS may pave the way for routine robust single voxel proteomics and spatial proteomics.https://doi.org/10.1038/s41467-024-54643-x |
| spellingShingle | Reta Birhanu Kitata Marija Velickovic Zhangyang Xu Rui Zhao David Scholten Rosalie K. Chu Daniel J. Orton William B. Chrisler Tong Zhang Jeremy V. Mathews Benjamin M. Bumgarner Demirkan B. Gursel Ronald J. Moore Paul D. Piehowski Tao Liu Richard D. Smith Huiping Liu Clive H. Wasserfall Chia-Feng Tsai Tujin Shi Robust collection and processing for label-free single voxel proteomics Nature Communications |
| title | Robust collection and processing for label-free single voxel proteomics |
| title_full | Robust collection and processing for label-free single voxel proteomics |
| title_fullStr | Robust collection and processing for label-free single voxel proteomics |
| title_full_unstemmed | Robust collection and processing for label-free single voxel proteomics |
| title_short | Robust collection and processing for label-free single voxel proteomics |
| title_sort | robust collection and processing for label free single voxel proteomics |
| url | https://doi.org/10.1038/s41467-024-54643-x |
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