PXD054765

PXD054765 is an original dataset announced via ProteomeXchange.

Title	Characterization of endosomes and interactions from TMEM230 and TMEM9/9B mutants in human neurons
Description	EndoMAP aims to systematically dissect the human endosomal protein complexes. To examine TMEM9 and TMEM230 interactions, we generated TMEM230 and TMEM9 knockouts (KOs) using CRISPR/Cas9 in human embryonic stem (ES) cells and converted the cells to induced neurons (iNeurons). TMEM230 and TMEM9 were immunoprecipitated (IP) on day-21 iNeurons and analyzed by TMT-MS, using the respective KOs as a negative control. In addition, TMEM230 immunoprecipitations were performed in TMEM230 KO iNeurons expressing WT and individual disease variant of TMEM230 (Y29C, R78L, and X121W), as well as a triple mutant carrying all three variants. To examine the impact of TMEM230 mutations and TMEM9/9B loss on total and endosomal proteome, we additionally generated TMEM230(X121W) and TMEM9/TMEM9B double knockout (DKO) in ES cells. The proteome of post-nuclear supernatant (PNS) and purified endosomes (Endo-IP) from WT, TMEM230 KO, and TMEM230(X121W) iNeurons were analyzed by TMT-MS. The proteome of PNS and purified endosomes (Endo-IP) from TMEM9 KO and two clones of TMEM9/9B DKO iNeurons were analyzed by TMT-MS.
HostingRepository	PRIDE
AnnounceDate	2025-05-30
AnnouncementXML	Submission_2025-05-30_02:37:41.575.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD054765
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Miguel A. Gonzalez-Lozano
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-09 12:23:50	ID requested
1	2025-03-29 12:25:20	announced
⏵ 2	2025-05-30 02:37:41	announced	2025-05-30: Updated project metadata.

10.1038/S41586-025-09059-Y;

10.6019/PXD054765;

submitter keyword: TMT, Human, TMEM9, Endosomes, iNeurons, TMEM230,EndoMAP

J. Wade Harper
contact affiliation	Department of Cell Biology, Harvard Medical School, Boston MA
contact email	wade_harper@hms.harvard.edu
lab head
Miguel A. Gonzalez-Lozano
contact affiliation	Department of Cell Biology, Harvard Medical School, Boston MA
contact email	miguel_gonzalezlozano@hms.harvard.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/2025/03/PXD054765

PRIDE project URI

• PRIDE
  1. PXD054765
     1. Label: PRIDE project
     2. Name: Characterization of endosomes and interactions from TMEM230 and TMEM9/9B mutants in human neurons