PXD032169

PXD032169 is an original dataset announced via ProteomeXchange.

Title	An Approach to Measuring Protein Turnover in Human Induced Pluripotent Stem Cell Organoids by Mass Spectrometry
Description	Patient-derived organoids from induced pluripotent stem cells have emerged as a model for studying human diseases beyond conventional two-dimensional (2D) cell culture. As such, the development of robust methods to study global proteostasis and protein turnover in organoids will remain essential as organoid models evolve. To solve this problem, we have designed a workflow to reproducibly extract proteins from brain organoids, measure global protein turnover using mass spectrometry, and statistically investigate turnover differences between genotypes. We also provide robust methodology for data filtering in turnover determination and for statistical treatment of turnover data. Using human midbrain organoids (hMO) as a model system, our method accurately characterized the half-lives of 773 midbrain proteins. We compared these half-lives both to Parkin knockout hMOs and to previously reported data from primary cell cultures and in vivo models. Taken together, this method will facilitate the study of proteostasis in organoid models of human disease and will provide an analytical and statistical framework to measure protein turnover in organoids of all cell types.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:45:24.609.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Bayne
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-09 02:36:15	ID requested
1	2024-06-15 23:31:48	announced
⏵ 2	2024-10-22 06:45:26	announced	2024-10-22: Updated project metadata.

Ross AB, Gorhe D, Kim JK, Hodapp S, DeVine L, Chan KM, Chio IIC, Jovanovic M, Ayres Pereira M, Systematic analysis of proteome turnover in an organoid model of pancreatic cancer by dSILO. Cell Rep Methods, 4(5):100760(2024) [pubmed]

10.1016/j.crmeth.2024.100760;

submitter keyword: midbrain organoid, midbrain, SILAC, half-life determination, turnover, d3-leucine, Topograph,organoid

Jean-Francois Trempe
contact affiliation	McGill University Department of Pharmacology and Therapeutics Centre de Recherche en Biologie Structurale
contact email	jeanfrancois.trempe@mcgill.ca
lab head
Andrew Bayne
contact affiliation	McGill University
contact email	andrew.bayne@mail.mcgill.ca
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/2024/06/PXD032169

PRIDE project URI

• PRIDE
  1. PXD032169
     1. Label: PRIDE project
     2. Name: An Approach to Measuring Protein Turnover in Human Induced Pluripotent Stem Cell Organoids by Mass Spectrometry