PXD042367-2

PXD042367 is an original dataset announced via ProteomeXchange.

Title	A framework for ultra-low input spatial tissue proteomics
Description	Spatial tissue proteomics combining microscopy-based cell phenotyping with ultrasensitive mass spectrometry (MS)-based proteomics is an emerging and powerful concept for the study of cell function and heterogeneity in health and disease. However, optimized workflows that preserve morphological information for image-based phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected archival tissue, are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low input formalin-fixed, paraffin-embedded (FFPE) material. Benchmarking in the murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions with high quantitative reproducibility. Applied to human tonsil, we profiled 146 microregions including spatially defined T and B lymphocyte niches and quantified cell-type specific markers, cytokines, immune cell regulators and transcription factors. These rich data also highlighted proteome dynamics in spatially defined zones of activated germinal centers, illuminating sites undergoing active B-cell proliferation and somatic hypermutation. Our results demonstrate the power of spatially-resolved proteomics for tissue phenotyping by integrating high-content imaging, laser microdissection, and ultrasensitive mass spectrometry. This approach has broad implications for a wide range of biomedical applications, including early disease profiling, drug target discovery and biomarker research.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:24:15.213.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fabian Coscia
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; 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	2023-05-20 08:03:30	ID requested
1	2023-11-08 05:40:40	announced
⏵ 2	2023-11-14 08:24:15	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Spatial proteomics, mass spectrometry, tissue profiling

Fabian Coscia
contact affiliation	Spatial Proteomics Max Delbrück Center Robert-Rössle-Straße 10 13125 Berlin, Germany
contact email	fabian.coscia@mdc-berlin.de
lab head
Fabian Coscia
contact affiliation	Max Delbrück Center
contact email	fabian.coscia@mdc-berlin.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/2023/11/PXD042367

PRIDE project URI

• PRIDE
  1. PXD042367
     1. Label: PRIDE project
     2. Name: A framework for ultra-low input spatial tissue proteomics