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PXD020586 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleQuantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies
DescriptionLarge-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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterErwin Schoof
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Exploris 480; Orbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-07-27 00:56:11ID requested
12021-05-05 22:20:40announced
22021-07-01 04:07:26announced2021-07-01: Updated publication reference for PubMed record(s): 34099695.
Publication List
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]
Keyword List
submitter keyword: LC-MS, TMTPro, scMS, single cell proteomics
Contact List
Bo Porse
contact affiliationThe 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 emailbo.porse@finsenlab.dk
lab head
Erwin Schoof
contact affiliationTechnical University of Denmark
contact emailerws@dtu.dk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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