PXD002959

PXD002959 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics
Description	Spatially targeted optical microproteomics (STOMP) is a novel proteomics technique for interrogating micron-scale regions of interest (ROI) in mammalian tissue, with no requirement for genetic manipulation. Methanol or formalin fixed specimens are stained with fluorescent dyes or antibodies to visualize ROIs, then soaked in solutions containing the photo-tag: 4-benzoylbenzyl-glycyl-hexahistidine. Confocal imaging along with two photon excitation are used to covalently couple photo-tags to all proteins within each ROI, to a resolution of 0.67 µm in the xy-plane and 1.48 µm axially. After tissue solubilization, photo-tagged proteins are isolated and identified by mass spectrometry. As a test case, we examined amyloid plaques in an Alzheimer’s disease (AD) mouse model and a postmortem AD case, confirming known plaque constituents and discovering new ones. STOMP can be applied to various biological samples including cell lines, primary cell cultures, ex vivo specimens, biopsy samples and fixed postmortem tissue.
HostingRepository	PRIDE
AnnounceDate	2015-11-18
AnnouncementXML	Submission_2015-11-18_08:34:23.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hongbo Guo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-22 02:00:05	ID requested
⏵ 1	2015-11-18 08:34:24	announced

Publication List

Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics. Elife, 4():(2015) [pubmed]

Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics. Elife, 4():(2015) [pubmed]

Keyword List

curator keyword: Biomedical
submitter keyword: neurodegenerative disease

curator keyword: Biomedical

submitter keyword: neurodegenerative disease

Contact List

Avijit Chakrabartty
contact affiliation	Professor
contact email	chakrab@uhnres.utoronto.ca
lab head
Hongbo Guo
contact affiliation	University of Toronto
contact email	hongboguo88@gmail.com
dataset submitter

Full Dataset Link List

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/2015/11/PXD002959
PRIDE project URI

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/2015/11/PXD002959

PRIDE project URI

Repository Record List

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