<<< Full experiment listing

PXD023904

PXD023904 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDeep Visual Proteomics defines single-cell identity and heterogeneity
DescriptionDespite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_09:01:06.094.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterFabian Coscia
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-31 22:59:28ID requested
12022-04-27 12:00:59announced
22023-06-16 02:42:22announced2023-06-16: Updated project metadata.
32023-11-14 09:01:08announced2023-11-14: Updated project metadata.
Publication List
Mund A, Coscia F, Kriston A, Hollandi R, Kov, รก, cs F, Brunner AD, Migh E, Schweizer L, Santos A, Bzorek M, Naimy S, Rahbek-Gjerdrum LM, Dyring-Andersen B, Bulkescher J, Lukas C, Eckert MA, Lengyel E, Gnann C, Lundberg E, Horvath P, Mann M, Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat Biotechnol, 40(8):1231-1240(2022) [pubmed]
Keyword List
submitter keyword: Microscopy, Digital Pathology,Proteomics, Laser Microdissection
Contact List
Matthias Mann
contact affiliationProf. Dr. Matthias Mann Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried +49 89 8578-2557
contact emailmmann@biochem.mpg.de
lab head
Fabian Coscia
contact affiliationMax Delbrueck Center for Molecular Medicine
contact emailfabian.coscia@cpr.ku.dk
dataset submitter
Full Dataset Link List
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/2022/04/PXD023904
PRIDE project URI
Repository Record List
[ + ]