PXD040084-2

PXD040084 is an original dataset announced via ProteomeXchange.

Title	Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation
Description	Cell-selective proteomics is emerging as a powerful concept for studying heterocellular processes. However, its potential to dissect intercellular signaling has not been exploited, despite its promise to identify non-cell autonomous disease mechanisms or biomarkers. Here, we devised an improved azidonorleucine-based protein labeling, enrichment, and mass spectrometry workflow, to achieve comprehensive proteome coverage of up to >10,100 cell-selective proteins. We provide proof-of-concept for in depth cell-selective secretomics by dissecting bidirectional intercellular signaling between co-cultured primary pancreatic ductal adenocarcinoma (PDAC) cells and macrophages. In vivo, detection of extracellular proteins emerged as a unique strength compared to FACS-based methods. Our analysis reveals systematic differences of cancer cell-derived matrisome proteins between molecular PDAC subtypes in vivo, such as elevated EMT-signal sustaining proteins. Intriguingly, high levels of pre-metastatic niche formation-associated factors in the serum reflected tumor activity in circulation. Our findings highlight how cell-selective proteomics accelerates the discovery of diagnostic markers and new therapeutic targets in cancer.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:04:01.882.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; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Exploris 480; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-13 01:25:25	ID requested
1	2023-07-20 17:28:49	announced
⏵ 2	2023-11-14 09:04:06	announced	2023-11-14: Updated project metadata.

Swietlik JJ, B, ä, rthel S, Falcomat, à C, Fink D, Sinha A, Cheng J, Ebner S, Landgraf P, Dieterich DC, Daub H, Saur D, Meissner F, Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation. Nat Commun, 14(1):2642(2023) [pubmed]

submitter keyword: submitter keyword: LC-MSMS, proteomics, cell-selective, azidonorleucine, secretomics, serum, mouse, tumor, PDAC, pancreatic cancer, extracellular matrix

Felix Meissner
contact affiliation	Experimental Systems Immunology Laboratory, Max Planck Institute of Biochemistry, Martinsried, Germany Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Germany (lab head)
contact email	felix.meissner@uni-bonn.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/2023/07/PXD040084

PRIDE project URI

• PRIDE
  1. PXD040084
     1. Label: PRIDE project
     2. Name: Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation