PXD016563

PXD016563 is an original dataset announced via ProteomeXchange.

Title	Laser-capture proteomics of human FFPE substantia nigra
Description	Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. In this study, we have developed an optimized protocol to facilitate efficient LCM analysis of FFPE tissue specimens. First, we optimized protein extraction from FFPE tissue by comparing different extraction buffers and investigating the influence of immunohistochemical and haematoxylin & eosin staining on proteins. SDS present in the protein extracts was removed with the SP3 digest method, which was modified to improve protein and peptide recoveries. Using a label-free approach protein expression of microdissected samples was compared to intact tissue sections from substantia nigra to evaluate the efficiency of LCM for the purification of small cell populations. The optimized protocol was used to analyse samples containing as few as ~3,000 cells isolated from the substantia nigra, using FFPE tissue. Replicate samples of 15 healthy donors were analysed in five separate TMT10plex batches, resulting in the quantification of >5,600 protein groups.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:59:09.403.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eva Griesser
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-04 02:58:17	ID requested
1	2020-03-05 07:08:42	announced
2	2020-06-12 01:49:43	announced	2020-06-12: Updated publication reference for PubMed record(s): 32132230.
⏵ 3	2024-10-22 04:59:17	announced	2024-10-22: Updated project metadata.

Griesser E, Wyatt H, Ten Have S, Stierstorfer B, Lenter M, Lamond AI, Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue. Mol Cell Proteomics, 19(5):839-851(2020) [pubmed]

10.1074/mcp.ra119.001889;

curator keyword: Technical, Biological

submitter keyword: laser-capture microdissection, TMT,FFPE, substantia nigra

Angus I. Lamond
contact affiliation	Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee
contact email	a.i.lamond@dundee.ac.uk
lab head
Eva Griesser
contact affiliation	Drug Discoverey Sciences Department, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
contact email	eva.griesser@boehringer-ingelheim.com
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/2020/03/PXD016563

PRIDE project URI

• PRIDE
  1. PXD016563
     1. Label: PRIDE project
     2. Name: Laser-capture proteomics of human FFPE substantia nigra