PXD044714

PXD044714 is an original dataset announced via ProteomeXchange.

Title	Spatial Proteomics of a Human Brain Tumour at 40 µm resolution
Description	The spatial organisation of Cellular protein expression profiles within tissues determines cellular function and are key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially resolved, quantitative proteomics of tissue that generates maps of protein expression across a tissue slice derived from a human atypical teratoid-rhabdoid tumour (AT/RT). We employ spatially-aware statistical methods that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with varying spatial abundance patterns. We identified PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response driven, spatially organized protein networks of the extracellular tumour matrix. Overall, this work informs on methods for spatially resolved deep proteo-phenotyping of tissue heterogeneity, which will push the boundaries of understanding tissue biology and pathology at the molecular level.
HostingRepository	PRIDE
AnnounceDate	2023-10-10
AnnouncementXML	Submission_2023-10-10_09:33:56.370.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	SimonDavis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-21 21:47:21	ID requested
⏵ 1	2023-10-10 09:33:56	announced

Dataset with its publication pending

submitter keyword: Spatial Proteomics, Laser Capture Microdissection,roteomics

RomanFischer
contact affiliation	Discovery Proteomics Lab, University of Oxford
contact email	roman.fischer@ndm.ox.ac.uk
lab head
SimonDavis
contact affiliation	University of Oxford
contact email	simon.davis2@ndm.ox.ac.uk
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/PXD044714

PRIDE project URI

• PRIDE
  1. PXD044714
     1. Label: PRIDE project
     2. Name: Spatial Proteomics of a Human Brain Tumour at 40 µm resolution