PXD038699-2

PXD038699 is an original dataset announced via ProteomeXchange.

Title	Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome
Description	Single-cell proteomics by mass spectrometry (MS) is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion of the method to complex tissues would greatly enhance biological insights. Here we describe single-cell Deep Visual Proteomics (scDVP), a technology that integrates high-content imaging, laser microdissection and multiplexed MS. scDVP resolves the context-dependent, spatial proteome of murine hepatocytes at a current depth of 1,700 proteins from a slice of a cell. Half of the proteome was differentially regulated in a spatial manner, with protein levels changing dramatically in proximity to the central vein. We applied machine learning to proteome classes and images, which subsequently inferred the spatial proteome from imaging data alone. scDVP is applicable to healthy and diseased tissues and complements other spatial proteomics or spatial omics technologies.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:37:35.098.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	dimethylated residue
Instrument	Bruker Daltonics timsTOF series; timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-08 16:38:03	ID requested
1	2023-10-03 10:35:16	announced
⏵ 2	2023-11-14 07:37:35	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Single-cell proteomics, machine learning, hepatocytes, tissue heterogeneity, spatial omics, liver

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD038699

PRIDE project URI

• PRIDE
  1. PXD038699
     1. Label: PRIDE project
     2. Name: Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome