PXD020933

PXD020933 is an original dataset announced via ProteomeXchange.

Title	Integrated Proteomic and Multi-Omic Characterizations of the Synapse Reveal RNA Processing Factors and Ubiquitin Ligases Associated with Neurodevelopmental Disorders
Description	The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models including the fetal human brain and hiPSC-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The integrated proteomic and multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 492 proteins that have not been documented previously. We further investigate three such proteins that are associated with neurodevelopmental disorders – the CUL3 E3 ubiquitin ligase, the DDX3X and YBX1 nucleic-acid binding factors – by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to systematically and more comprehensively resolve the synaptic architecture.
HostingRepository	PRIDE
AnnounceDate	2026-03-09
AnnouncementXML	Submission_2026-03-08_17:54:56.781.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brent Wilkinson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-16 23:05:03	ID requested
⏵ 1	2026-03-08 17:54:57	announced

10.1016/j.cels.2025.101204;

Mei Y, Gosztyla ML, Tan X, Dozier LE, Wilkinson B, McKetney J, Lee J, Chen M, Tsai D, Kopalle H, Gritsenko MA, Hartel N, Graham NA, Flores I, Gilmore-Hall SK, Xu S, Marquez CA, Liu SN, Fong D, Chen J, Licon K, Hong D, Wright SN, Kreisberg JF, Nott A, Smith RD, Qian WJ, Swaney DL, Iakoucheva LM, Krogan NJ, Patrick GN, Zhou Y, Feng G, Coba MP, Yeo GW, Ideker T, Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. Cell Syst, 16(4):101204(2025) [pubmed]

submitter keyword: Induced Neurons, Synaptic, Fetal Brain, PSD

Marcelo Coba
contact affiliation	Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA
contact email	coba@usc.edu
lab head
Brent Wilkinson
contact affiliation	University of Southern California
contact email	brentwil@usc.edu
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/2026/03/PXD020933

PRIDE project URI

• PRIDE
  1. PXD020933
     1. Label: PRIDE project
     2. Name: Integrated Proteomic and Multi-Omic Characterizations of the Synapse Reveal RNA Processing Factors and Ubiquitin Ligases Associated with Neurodevelopmental Disorders