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PXD028150-1

PXD028150 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleInterrogating kinase-substrate relationships with proximity labeling and phosphorylation enrichment
DescriptionKinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase “ON” and kinase “OFF” conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification. TMT1: pAPEX-MAPK1 experiment in HEK293T cells TMT2: pAPEX-MAPK1 experiment in HCT116 cells TMT3: pAPEX-PKA experiment in HEK293T cells
HostingRepositoryPRIDE
AnnounceDate2022-03-11
AnnouncementXMLSubmission_2022-03-11_11:09:35.453.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTian Zhang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-08-26 04:06:39ID requested
12022-03-11 11:09:35announced
22023-11-14 08:54:18announced2023-11-14: Updated project metadata.
Publication List
10.1021/ACS.JPROTEOME.1C00865;
Keyword List
submitter keyword: Proximity labeling, APEX, Kinases, substrates, MAPK1, PKA
Contact List
Steven Gygi
contact affiliationCell Biology Department, Harvard Medical School
contact emailsteven_gygi@hms.harvard.edu
lab head
Tian Zhang
contact affiliationHarvard Medical School
contact emailtian_zhang@hms.harvard.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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