PXD009783-2

PXD009783 is an original dataset announced via ProteomeXchange.

Title	Proteomic proximity mapping by rapamycin-dependent targeting of APEX2
Description	Enhanced ascorbate peroxidase 2 (APEX2) can be used as a genetic tag that produces short-lived yet highly reactive biotin species, allowing the modification of proteins that interact with or are in very close proximity to the tagged protein, ideally within a confined compartment. Biotinylated proteins can be isolated using immobilized streptavidin and analyzed by mass spectrometry. Here we used rapamycin-dependent targeting of APEX2 to tail-anchored proteins of the endoplasmic reticulum and of the inner nuclear membrane (INM). In combination with stable isotope labeling with amino acids in cell culture (SILAC), our novel approach (rapamycin- and APEX-dependent identification of proteins by SILAC; RAPID-SILAC or RAPIDS) allowed the identification of proteins that are in close proximity to the prototypic INM-protein emerin and the vesicle-trafficking protein VAPB. In addition to well-known interaction partners, several new potential binding partners were identified. In RAPIDS, the comparison of plus/minus-rapamycin conditions allows a clear distinction between specific and non-specific hits.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:02:02.360.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christof Lenz
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-15 03:27:52	ID requested
1	2020-04-15 01:22:24	announced
⏵ 2	2024-10-22 05:02:10	announced	2024-10-22: Updated project metadata.

10.3390/cells9030605;

M, ü, ller M, James C, Lenz C, Urlaub H, Kehlenbach RH, Probing the Environment of Emerin by Enhanced Ascorbate Peroxidase 2 (APEX2)-Mediated Proximity Labeling. Cells, 9(3):(2020) [pubmed]

curator keyword: Technical

submitter keyword: APEX2, mass spectrometry, proximity labeling, SILAC,APEX

Christof Lenz
contact affiliation	University Medical Center Göttingen, Institute of Clinical Chemistry
contact email	christof.lenz@med.uni-goettingen.de
lab head
Christof Lenz
contact affiliation	Max Planck Institute for Biophysical Chemistry
contact email	christof.lenz@mpibpc.mpg.de
dataset submitter

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/2020/04/PXD009783

PRIDE project URI

• PRIDE
  1. PXD009783
     1. Label: PRIDE project
     2. Name: Proteomic proximity mapping by rapamycin-dependent targeting of APEX2