MassIVE MSV000091531

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A comprehensive evaluation of common quantification strategies for LC-MS/MS-based spatial proteomics using nanoPOTS

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Description

A deep understanding of the tissue microenvironment can provide significant insight into the function of tissue and organs in health and disease states. Spatially resolved proteomics techniques can aid in studying spatial tissue organization and cellular communication in their native microenvironment. However, current spatial proteomics technologies using antibody-based methods or mass spectrometry imaging cannot achieve deep proteome coverage. Bottom-up or global proteomics can offer deep coverage of >5000 proteins, but the low sample amount and inefficient workflow limit both proteome coverage and spatial resolution. To overcome these limitations, we developed and evaluated two MS sample preparation and data acquisition strategies coupled with our nanoPOTS-LCM-based spatial proteomics workflow. We compared label-free sample preparation with a 3D matching approach and multiplexed isobaric labeling with improved MS/MS data acquisition. Our study demonstrates the capability of nanoPOTS-based spatial proteomics in mapping the human pancreas at near single-cell resolution, enabling the visualization of protein expression patterns and the discovery of spatially co-expressed proteins in their tissue context. [doi:10.25345/C5KP7V20K] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: spatially-resolved proteomics ; LCM ; nanoPOTS

Contact

Principal Investigators:
(in alphabetical order) 		Ying Zhu, Genentech, United States
Submitting User: alchemistmatt

Publications

Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y.
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows.
Mol Cell Proteomics. Epub 2024 Sep 20.

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