PXD058457

PXD058457 is an original dataset announced via ProteomeXchange.

Title	High throughput single-cell proteomics of in-vivo cells
Description	Major advancements in single-cell proteomics (SCP) methodologies have been introduced in recent years, providig highly sensitive sample preparation methods and mass spectrometric technologies. However, most studies present limited throughput and mainly focus on the analysis of cultured cells. To enhance the depth, accuracy, and throughput of SCP for tumor analysis, we developed an automated, high-throughput pipeline that enables the analysis of 1,536 single cells in a single experiment. This approach integrates low-volume sample preparation, automated sample purification, and LC-MS analysis with the Slice-PASEF method. Integration of these methodologies into a streamlined pipeline led to a robust and reproducible identification of more than 3000 proteins per cell. We applied this pipeline to analyze tumor macrophages in a murine lung metastasis model. We identified over 1,800 proteins per cell, including key macrophage markers and ~500 differentially expressed proteins between tumor and control macrophages. PCA analysis successfully separated these populations, revealing the utility of SCP in capturing biologically relevant signals in the tumor microenvironment. Our results demonstrate a robust and scalable pipeline poised to advance single-cell proteomics in cancer research.
HostingRepository	PRIDE
AnnounceDate	2025-07-12
AnnouncementXML	Submission_2025-07-12_13:24:12.491.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tamar Geiger
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-01 23:24:13	ID requested
⏵ 1	2025-07-12 13:24:12	announced

10.1016/J.MCPRO.2025.101018;

submitter keyword: Macrophages,Single Cell Proteomics, Fixation, Murine, LC-MS, HeLa, Bravo, Slice-PASEF, timsTOF, Automation

Tamar Geiger
contact affiliation	Molecular Cell Biology, Weizmann Institute of Science
contact email	tami.geiger@weizmann.ac.il
lab head
Tamar Geiger
contact affiliation	Weizmann Institute of Science
contact email	geiger@tauex.tau.ac.il
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/2025/07/PXD058457

PRIDE project URI

• PRIDE
  1. PXD058457
     1. Label: PRIDE project
     2. Name: High throughput single-cell proteomics of in-vivo cells