PXD045840

PXD045840 is an original dataset announced via ProteomeXchange.

Title	A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology
Description	Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell SPAtially resolved METabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet pipeline to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil and endometrium tissues, respectively. ScSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:14:40.659.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	THOMAS HU
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	mass spectrometry imaging

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-01 10:50:35	ID requested
⏵ 1	2024-10-08 11:14:41	announced

Dataset with its publication pending

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: Human Lung, endometrium IMC imaging, tumor

Thomas Hu
contact affiliation	Georgia Institute of Technology
contact email	thu71@gatech.edu
lab head
THOMAS HU
contact affiliation	Georgia Institute of Technology
contact email	thu71@gatech.edu
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/PXD045840

PRIDE project URI

• PRIDE
  1. PXD045840
     1. Label: PRIDE project
     2. Name: A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology