PXD012101

PXD012101 is an original dataset announced via ProteomeXchange.

Title	Development of a sensitive, scalable method for spatial, cell-type-resolved proteomics of the human brain
Description	While nearly comprehensive proteome coverage can be achieved from bulk tissue or cultured cells, the data usually lacks spatial resolution. As a result, tissue based proteomics averages protein abundance across multiple cell types and/or localisations. With proteomics platforms lacking sensitivity and throughput to undertake deep single-cell proteome studies to resolve spatial or cell type dependent protein expression gradients within tissue, proteome analysis has been combined with sorting techniques to enrich for certain cell populations. However, the tissue context and spatial resolution is lost in the sorting process. Here, we report an optimised method for the proteomic analysis of neurons isolated from post-mortem human brain by Laser Capture Microdissection (LCM). We tested combinations of sample collection methods, lysis buffers and digestion methods to maximize the number of identifications and quantitative performance, identifying up to 1500 proteins from 60,000 µm2 of cerebellar molecular layer with excellent reproducibility. In order to demonstrate the ability of our workflow to resolve for the first time cell type specific proteomes within a tissue, we isolated sets of individual Betz and Purkinje cells. Both neuronal cell types are involved in motor coordination and were found to express highly specific proteomes to a depth of 2800 to 3600 proteins.
HostingRepository	PRIDE
AnnounceDate	2019-03-04
AnnouncementXML	Submission_2019-03-04_05:31:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simon Davis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-18 08:56:42	ID requested
⏵ 1	2019-03-04 05:31:24	announced

Davis S, Scott C, Ansorge O, Fischer R, Development of a Sensitive, Scalable Method for Spatial, Cell-Type-Resolved Proteomics of the Human Brain. J Proteome Res, 18(4):1787-1795(2019) [pubmed]

submitter keyword: LC-MS/MS, Laser Capture Microdissection, Tissue Proteomics, Spatially Resolved Proteomics, Brain

Roman Fischer
contact affiliation	1Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
contact email	roman.fischer@ndm.ox.ac.uk
lab head
Simon Davis
contact affiliation	University of Oxford
contact email	simon.davis2@ndm.ox.ac.uk
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/2019/03/PXD012101

PRIDE project URI

• PRIDE
  1. PXD012101
     1. Label: PRIDE project
     2. Name: Development of a sensitive, scalable method for spatial, cell-type-resolved proteomics of the human brain