PXD051016-2

PXD051016 is an original dataset announced via ProteomeXchange.

Title	Proteome dynamics in iPSC-derived human dopaminergic neurons – part 3: dynamic SILAC to study local synthesis and trafficking of proteins
Description	Dopaminergic neurons participate in fundamental physiological processes and are the cell type primarily affected in Parkinson’s disease (PD). Their analysis is challenging due to the intricate nature of their function, their involvement in diverse neurological processes, their heterogeneity and localization in deep brain regions. Consequently, most of the research on the protein dynamics of dopaminergic neurons has been performed in animal cells ex vivo. Here we use iPSC-derived, human mid-brain specific dopaminergic neurons to study general features of their proteome biology. We use differential dynamic SILAC labeling in combination with microfluidic devices to analyze local protein synthesis and transport between axons and soma. We report 105 potentially novel axonal markers and detect translocation of 269 proteins between axons and the soma in the time frame of our analysis (120 hours). Importantly, we provide evidence for local synthesis of 154 proteins in the axon and their retrograde transport to the soma. Our study provides a workflow and resource for future applications of quantitative proteomics in iPSC-derived human neurons
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:58:05.430.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Claudia Cavarischia Rega
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-27 06:56:58	ID requested
1	2024-09-12 02:10:53	announced
⏵ 2	2024-10-22 06:58:05	announced	2024-10-22: Updated project metadata.

10.1016/J.MCPRO.2024.100838;

submitter keyword: proteomics, iPSC, axon,dopaminergic neurons, protein turnover

Boris Macek
contact affiliation	Quantitative Proteomics Director, Proteome Center Tuebingen Institute for Cell Biology University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen
contact email	boris.macek@uni-tuebingen.de
lab head
Claudia Cavarischia Rega
contact affiliation	Proteome Center Tuebingen Interfaculty Institute for Cell Biology University of Tuebingen
contact email	claudia.cavarischia-rega@uni-tuebingen.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/2024/09/PXD051016

PRIDE project URI

• PRIDE
  1. PXD051016
     1. Label: PRIDE project
     2. Name: Proteome dynamics in iPSC-derived human dopaminergic neurons – part 3: dynamic SILAC to study local synthesis and trafficking of proteins