Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive Plus

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Ying Zhu

PROVIDER: MSV000089295 | MassIVE | Thu Apr 21 14:53:00 BST 2022

REPOSITORIES: MassIVE

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Hanging drop sample preparation improves sensitivity of spatial proteomics.

Kwon Yumi Y Piehowski Paul D PD Zhao Rui R Sontag Ryan L RL Moore Ronald J RJ Burnum-Johnson Kristin E KE Smith Richard D RD Qian Wei-Jun WJ Kelly Ryan T RT Zhu Ying Y

Lab on a chip 20220726 15

Spatial proteomics holds great promise for revealing tissue heterogeneity in both physiological and pathological conditions. However, one significant limitation of most spatial proteomics workflows is the requirement of large sample amounts that blurs cell-type-specific or microstructure-specific information. In this study, we developed an improved sample preparation approach for spatial proteomics and integrated it with our previously-established laser capture microdissection (LCM) and microflu ...[more]

PMID: 35838077

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