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PXD032169

PXD032169 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAn Approach to Measuring Protein Turnover in Human Induced Pluripotent Stem Cell Organoids by Mass Spectrometry
DescriptionPatient-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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:45:24.609.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAndrew Bayne
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-03-09 02:36:15ID requested
12024-06-15 23:31:48announced
22024-10-22 06:45:26announced2024-10-22: Updated project metadata.
Publication List
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;
Keyword List
submitter keyword: midbrain organoid, midbrain, SILAC, half-life determination, turnover, d3-leucine, Topograph,organoid
Contact List
Jean-Francois Trempe
contact affiliationMcGill University Department of Pharmacology and Therapeutics Centre de Recherche en Biologie Structurale
contact emailjeanfrancois.trempe@mcgill.ca
lab head
Andrew Bayne
contact affiliationMcGill University
contact emailandrew.bayne@mail.mcgill.ca
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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