Proteomics

Dataset Information

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A standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics


ABSTRACT: Defining the molecular phenotype of single cells in-situ is essential for understanding tissue heterogeneity in health and disease. Powerful imaging technologies have recently been joined by spatial omics technologies, promising unparalleled insights into the molecular landscape of biological samples. One approach involves laser microdissection in combination with membrane glass slides for the isolation of single cells from specific anatomical regions for further analysis by spatial omics. However, so far this is not fully compatible with automated staining platforms and routine histology procedures such as heat-induced epitope retrieval, limiting reproducibility, throughput and integration of advanced staining procedures. This study describes a robust workflow for routine use of glass membrane slides, allowing precise extraction of tissue in combination with automated and multicolor immunofluorescence staining. The key advance is the addition of glycerol to standard heat-induced epitope retrieval protocol, preventing membrane distortion while preserving antigen retrieval properties. Importantly, we show that glycerol is fully compatible with mass-spectrometry based proteomics and does not affect proteome depth or quality. Further, we enable single focal plane imaging by removing remaining trapped air pockets with an incision. We demonstrate our workflow using the recently introduced Deep Visual Proteomics technology on the single-cell type analysis of adjacent suprabasal and basal keratinocytes of human skin. Our protocol extends the utility of membrane glass slides and enables much more robust integration with routine histology procedures, high-throughput multiplexed imaging and sophisticated downstream spatial omics technologies.

INSTRUMENT(S): timsTOF Pro 2, timsTOF SCP

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Tonsil, Keratinocyte, Skin

SUBMITTER: Mario Oroshi  

LAB HEAD: Matthias Mann

PROVIDER: PXD040281 | Pride | 2023-10-24

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Bulk.zip Other
Bulk_MaxQuant_peptides.txt Txt
Bulk_MaxQuant_proteinGroups.txt Txt
DVP.zip Other
DVP_DIANN_report.pg_matrix.tsv Tabular
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Publications

A Standardized and Reproducible Workflow for Membrane Glass Slides in Routine Histology and Spatial Proteomics.

Nordmann Thierry M TM   Schweizer Lisa L   Metousis Andreas A   Thielert Marvin M   Rodriguez Edwin E   Rahbek-Gjerdrum Lise Mette LM   Stadler Pia-Charlotte PC   Bzorek Michael M   Mund Andreas A   Rosenberger Florian A FA   Mann Matthias M  

Molecular & cellular proteomics : MCP 20230907 10


Defining the molecular phenotype of single cells in situ is key for understanding tissue architecture in health and disease. Advanced imaging platforms have recently been joined by spatial omics technologies, promising unparalleled insights into the molecular landscape of biological samples. Furthermore, high-precision laser microdissection (LMD) of tissue on membrane glass slides is a powerful method for spatial omics technologies and single-cell type spatial proteomics in particular. However,  ...[more]

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