PXD040281-1

PXD040281 is an original dataset announced via ProteomeXchange.

Title	A standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics
Description	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.
HostingRepository	PRIDE
AnnounceDate	2023-10-24
AnnouncementXML	Submission_2023-10-24_14:36:09.616.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	MarioOroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF SCP; timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-20 07:05:20	ID requested
⏵ 1	2023-10-24 14:36:11	announced
2	2023-11-14 09:12:48	announced	2023-11-14: Updated project metadata.

Nordmann TM, Schweizer L, Metousis A, Thielert M, Rodriguez E, Rahbek-Gjerdrum LM, Stadler PC, Bzorek M, Mund A, Rosenberger FA, Mann M, A Standardized and Reproducible Workflow for Membrane Glass Slides in Routine Histology and Spatial Proteomics. Mol Cell Proteomics, 22(10):100643(2023) [pubmed]

submitter keyword: Antigen retrieval, Spatial proteomics, Deep Visual Proteomics, Glycerol, Membrane slides,Histology, Proteomics, Heat-induced epitope retrieval, Laser microdissection

MatthiasMann
contact affiliation	Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
MarioOroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040281
     1. Label: PRIDE project
     2. Name: A standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics