PXD027456-2

PXD027456 is an original dataset announced via ProteomeXchange.

Title	Proteomic Characterization of Post-Mortem Human Brain Tissue Following Ultracentrifugation-based Subcellular Fractionation
Description	Proteomic characterization of human brain tissue is increasingly utilized to identify potential novel biomarker and drug targets for a variety of neurological diseases. In whole tissue studies, results may be driven by changes in the proportion of the largest and most abundant organelles or tissue cell-type composition. Spatial proteomics approaches enhance our knowledge of disease mechanisms and changing signaling pathways at the subcellular level by taking into account the importance of cellular localization, which critically influences protein function. Density gradient-based ultracentrifugation methods allow for subcellular fractionation and have been utilized in cell lines and fresh mouse brain tissue to predict the subcellular location of thousands of proteins, but to our knowledge have not been used in frozen human brain tissue. The use of frozen human tissue for tissue fractionation faces two major challenges, the post-mortem interval, during which proteins may leach from their usual location into the cytosol, and freezing, which results in membrane breakdown. Despite these challenges, in this proof-of-concept study, we show that the majority of proteins segregate reproducibly into crude density-based centrifugation fractions, that the fractions are enriched for the appropriate organellar markers, and that significant differences in protein localization can be observed between tissue from individuals with Alzheimer’s Disease and control individuals.
HostingRepository	PRIDE
AnnounceDate	2024-11-12
AnnouncementXML	Submission_2024-11-12_05:31:15.842.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	TuKiet Lam
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-20 22:48:10	ID requested
1	2022-05-06 07:43:46	announced
⏵ 2	2024-11-12 05:31:16	announced	2024-11-12: Updated project metadata.

10.1093/braincomms/fcac103;

Kandigian SE, Ethier EC, Kitchen RR, Lam TT, Arnold SE, Carlyle BC, Proteomic characterization of post-mortem human brain tissue following ultracentrifugation-based subcellular fractionation. Brain Commun, 4(3):fcac103(2022) [pubmed]

submitter keyword: Subcellular Fractionation,Human Brain, Label Free Quantitation, Alzheimer's Disease

TuKiet Lam
contact affiliation	Yale University
contact email	tukiet.lam@yale.edu
lab head
TuKiet Lam
contact affiliation	Yale University
contact email	tukiet.lam@yale.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/2022/05/PXD027456

PRIDE project URI

• PRIDE
  1. PXD027456
     1. Label: PRIDE project
     2. Name: Proteomic Characterization of Post-Mortem Human Brain Tissue Following Ultracentrifugation-based Subcellular Fractionation