PXD020586-2

PXD020586 is an original dataset announced via ProteomeXchange.

Title	Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies
Description	Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes global single-cell mass spectrometry-based proteomics as a tool for large-scale single-cell analyses. By exploiting a primary leukemia model system, we demonstrate both through pre-enrichment of cell populations and through a non-enriched unbiased approach that our workflow enables the exploration of cellular heterogeneity within this aberrant developmental hierarchy. Our approach is capable of consistently quantifying approximately 1000 proteins per cell across thousands of individual cells using limited instrument time. Furthermore, we developed a computational workflow (SCeptre) that effectively normalizes the data, integrates available FACS data and facilitates downstream analysis. The approach presented here lays a solid foundation for implementing global single-cell proteomics studies across the world.
HostingRepository	PRIDE
AnnounceDate	2021-05-06
AnnouncementXML	Submission_2021-07-01_04:07:25.882.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erwin Schoof
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-27 00:56:11	ID requested
1	2021-05-05 22:20:40	announced
⏵ 2	2021-07-01 04:07:26	announced	2021-07-01: Updated publication reference for PubMed record(s): 34099695.

Schoof EM, Furtw, ä, ngler B, Ü, resin N, Rapin N, Savickas S, Gentil C, Lechman E, Keller UAD, Dick JE, Porse BT, Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nat Commun, 12(1):3341(2021) [pubmed]

submitter keyword: LC-MS, TMTPro, scMS, single cell proteomics

Bo Porse
contact affiliation	The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
contact email	bo.porse@finsenlab.dk
lab head
Erwin Schoof
contact affiliation	Technical University of Denmark
contact email	erws@dtu.dk
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/2021/05/PXD020586

PRIDE project URI

• PRIDE
  1. PXD020586
     1. Label: PRIDE project
     2. Name: Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies