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PXD039005 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleElucidating Fibroblast Growth Factor-induced kinome dynamics using targeted mass spectrometry and dynamic modeling
DescriptionFibroblast growth factors (FGFs) are paracrine or endocrine signaling proteins that when activated by their ligands, can elicit a wide range of healthy and disease-related processes such as cell proliferation and the epithelial-to-mesenchymal transition (EMT). The detailed molecular pathway dynamics that coordinate these responses have remained unclear. To elucidate and monitor these dynamics, we stimulated MCF-7 breast cancer cells with either FGF2, 3, 4, 10, or 19. Following activation of the receptor, we quantified the kinase activity dynamics of 44 kinases using a targeted mass spectrometry assay. Our system-wide kinase activity data, supplemented with (phopsho)proteomics data, reveal ligand-dependent distinct pathway dynamics, elucidate the involvement of not earlier reported kinases such as MARK, and revise some of the pathway effects on biological outcomes. In addition, logic-based dynamic modeling of the kinome dynamics further verifies the biological goodness-of-fit of the predicted models and reveals tight regulation of the RAF kinase family.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterTim Veth
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListPhospho; Carbamidomethyl; Oxidation; Label:13C(6)15N(2); Label:13C(6)15N(4); Label:13C(6)15N(1); Label:13C(5)15N(1)
InstrumentTSQ Altis
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-12-20 22:25:23ID requested
12023-07-02 08:29:50announced
Publication List
Veth TS, Francavilla C, Heck AJR, Altelaar M, Elucidating Fibroblast Growth Factor-Induced Kinome Dynamics Using Targeted Mass Spectrometry and Dynamic Modeling. Mol Cell Proteomics, 22(8):100594(2023) [pubmed]
Keyword List
submitter keyword: Phosphoproteomics, kinase, targeted mass spectrometry, kinase dynamics, fibroblast growth factors, dynamic modeling, fibroblast growth factor receptor, breast cancer. 
Contact List
Maarten Altelaar
contact affiliationUtrecht University, Netherlands Proteomics Center
contact emailm.altelaar@uu.nl
lab head
Tim Veth
contact affiliationBiomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht. Netherlands Proteomics Center.
contact emailt.s.veth@uu.nl
dataset submitter
Full Dataset Link List
Panorama Public dataset URI