PXD056902-1

PXD056902 is an original dataset announced via ProteomeXchange.

Title	Multiplexed phosphoproteomics of low cell numbers using SPARCE
Description	Understanding cellular diversity and disease mechanisms requires global analysis of proteins and their modifications. Ultrasensitive mass spectrometry-based proteomics enables unbiased protein-level analysis of low cell numbers, down to single cells. However, phosphoproteomics remains limited to high-input samples due to sample losses and poor reaction efficiencies associated with processing low cell numbers. In this study, we have used isobaric stable isotope labelling as a promising approach for reproducible and accurate quantification of low abundant phosphopeptides. Here, we introduce SPARCE (Streamlined Phosphoproteomic Analysis of Rare CElls) for multiplexed phosphoproteomic analysis of low cell numbers. SPARCE outperforms traditional methods by enhancing labelling efficiency and phosphoproteome coverage. To demonstrate the utility of SPARCE, we analysed four patient-derived glioblastoma stem cell lines, reliably quantifying phosphosite changes from 1,000 FACS-sorted cells. This workflow expands the possibilities for signalling analysis of rare cell populations.
HostingRepository	PRIDE
AnnounceDate	2025-04-01
AnnouncementXML	Submission_2025-04-01_09:44:12.012.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Silvia Surinova
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Exploris 480; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-17 05:04:24	ID requested
⏵ 1	2025-04-01 09:44:12	announced

Dataset with its publication pending

submitter keyword: TMT,Glioblastoma, Phospho, Low-input

Silvia Surinova
contact affiliation	Team Lead in Proteomics Head of the Proteomics Research Translational Technology Platform UCL Cancer Institute, Paul O’Gorman Building 72 Huntley Street, London, WC1E 6DD, UK
contact email	s.surinova@ucl.ac.uk
lab head
Silvia Surinova
contact affiliation	UCL
contact email	s.surinova@ucl.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD056902
     1. Label: PRIDE project
     2. Name: Multiplexed phosphoproteomics of low cell numbers using SPARCE