Proteomics

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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Ying Zhu  

PROVIDER: MSV000091531 | MassIVE | Wed Mar 22 18:58:00 GMT 2023

REPOSITORIES: MassIVE

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Publications

Proteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows.

Kwon Yumi Y   Woo Jongmin J   Yu Fengchao F   Williams Sarah M SM   Markillie Lye Meng LM   Moore Ronald J RJ   Nakayasu Ernesto S ES   Chen Jing J   Campbell-Thompson Martha M   Mathews Clayton E CE   Nesvizhskii Alexey I AI   Qian Wei-Jun WJ   Zhu Ying Y  

Molecular & cellular proteomics : MCP 20240920 11

Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteo  ...[more]

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