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Novel protocol for spatial proteome analysis of formalin fixed paraffin embedded tissues

ABSTRACT: Novel In-insert FFPE proteomics combines single glass insert FFPE tissue processing with spatial quantitative data-independent mass spectrometry (DIA). In-insert proteomics represents a blueprint in spatial FFPE tissue subsection processing by completely omitting the robotic platform, desalting prior to injection to the liquid chromatograph and detergent removal while restraining protein losses to the minimum. In-insert proteomics has a sufficient sensitivity to preserve spatial context within a single FFPE tissue slide. Spatial pathway regulation trends were evaluated between 17 individual breast tissue voxels by the method. Bioinformatic spatial analysis of the most dysregulated proteins was performed to reveal hotspots of certain biochemical signaling/processes. A special attention was given to cytoskeleton reorganization as an effect of hormone signaling.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast

DISEASE(S): Breast Cancer

SUBMITTER: Jakub Faktor

LAB HEAD: Sachin Kote

PROVIDER: PXD037609 | Pride | 2024-04-19

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	220614_DDA_PTLIM_10_3ul_120min.raw	Raw
	220614_DDA_PTLIM_10_3ul_120min_COMET.pep.xml	Pepxml
	220614_DDA_PTLIM_10_3ul_120min_FRAGGER.pep.xml	Pepxml
	220614_DDA_PTLIM_10_3ul_120min_FRAGGER_CRYSTAL-C_RECALCULATED_OPEN_SEARCH.pepXML	Pepxml
	220614_DDA_PTLIM_10_3ul_120min_FRAGGER_OPEN_SEARCH.pepXML	Pepxml

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