MassIVE MSV000089295

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Hanging-droplet sample preparation improves coverage for spatially-resolved proteomics

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Description

We developed a hanging drop (HD) method to improve the sample recovery for spatial proteomics by placing the nanowell chip in an upside-down direction during droplet-based sample preparation. Compared with the commonly-used sitting-drop (SD) method, the HD method can keep the tissue voxel away from the solid container surface, and thus improve the accessibility of the extraction buffer to tissue voxel. We demonstrated that the HD method could increase MS signal by 7x, leading to a 66% improvement in protein identification, in comparison to the SD method. An average of 721, 1489, and 2521 proteins can be quantitatively profiled from laser-dissected mouse liver tissue voxels with areas of 0.0025, 0.01, and 0.04 mm2, respectively. As a proof-of-concept study, the improved system was applied to study the cell-type-specific proteomes of mouse uterine sections. [doi:10.25345/C5XD0R220] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: nanoPOTS ; LCM ; spatially-resolved proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Ying Zhu, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Yumi Kwon, Paul D Piehowski, Rui Zhao, Ryan L Sontag, Ronald J Moore, Kristin E Burnum-Johnson, Richard D Smith, Wei-Jun Qian, Ryan T Kelly, Ying Zhu.
Hanging drop sample preparation improves sensitivity of spatial proteomics.
Lab Chip . 2022 Jul 15. doi: 10.1039/d2lc00384h.

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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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