PXD038947 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Hybrid-DIA: Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids |
Description | Achieving 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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_05:45:47.986.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Ana Martinez-Val |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-12-19 06:07:14 | ID requested | |
1 | 2023-05-18 06:03:24 | announced | |
2 | 2023-08-09 06:48:04 | announced | 2023-08-09: Updated project metadata. |
3 | 2023-11-14 09:04:37 | announced | 2023-11-14: Updated project metadata. |
⏵ 4 | 2024-10-22 05:45:48 | announced | 2024-10-22: 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 affiliation | Vice Director, Professor Novo Nordisk Foundation Center for Protein Research University of Copenhagen Faculty of Health and Medical Sciences Copenhagen, Denmark |
contact email | jesper.olsen@cpr.ku.dk |
lab head | |
Ana Martinez-Val |
contact affiliation | Novo Nordisk Foundation Center for Protein Research |
contact email | ana.mdval@cpr.ku.dk |
dataset submitter | |
Full Dataset Link List
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/2023/05/PXD038947 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD038947
- Label: PRIDE project
- Name: Hybrid-DIA: Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids