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PXD038947

PXD038947 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHybrid-DIA: Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids
DescriptionAchieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging when analyzing tiny sample amounts. We present a novel hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem MS scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmarked hybrid-DIA against state-of-the-art targeted MS methods (i.e. SureQuant) using EGF-stimulated HeLa cells and found the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiled the global phosphoproteome. To demonstrate the robustness, sensitivity and potential of hybrid-DIA, we profiled chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluated the difference of cancer cells in 2D vs 3D culture. Altogether, we showed that hybrid-DIA is the way-to-go method in highly sensitive phospho-proteomics experiments.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:45:47.986.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAna Martinez-Val
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-12-19 06:07:14ID requested
12023-05-18 06:03:24announced
22023-08-09 06:48:04announced2023-08-09: Updated project metadata.
32023-11-14 09:04:37announced2023-11-14: Updated project metadata.
42024-10-22 05:45:48announced2024-10-22: Updated project metadata.
Publication List
Mart, í, nez-Val A, Fort K, Koenig C, Van der Hoeven L, Franciosa G, Moehring T, Ishihama Y, Chen YJ, Makarov A, Xuan Y, Olsen JV, Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nat Commun, 14(1):3599(2023) [pubmed]
10.1038/s41467-023-39347-y;
Keyword List
submitter keyword: Phosphoproteomics,Targeted, Discovery, Proteomics, Spheroids
Contact List
Jesper Velgaard Olsen
contact affiliationVice Director, Professor Novo Nordisk Foundation Center for Protein Research University of Copenhagen Faculty of Health and Medical Sciences Copenhagen, Denmark
contact emailjesper.olsen@cpr.ku.dk
lab head
Ana Martinez-Val
contact affiliationNovo Nordisk Foundation Center for Protein Research
contact emailana.mdval@cpr.ku.dk
dataset submitter
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Dataset FTP location
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PRIDE project URI
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