PXD051706

PXD051706 is an original dataset announced via ProteomeXchange.

Title	Novel protocol for spatial proteome analysis of microdissected formalin-fixed paraffin-embedded tissues
Description	Novel In-insert FFPE proteomics combines single glass insert FFPE tissue processing with spatial quantitative data-independent mass spectrometry (DIA). The method represents a potent protocol for spatial FFPE tissue subsection processing in combination with laser capture microdissection, achieving sufficient MS signal from 50 um size mammary acini FFPE voxels. By eliminating additional robotic platforms, desalting and detergent removal steps prior to injection to the liquid chromatograph, this method minimizes protein losses and keep the analysis cost effective. In-insert proteomics maintains sufficient sensitivity to preserve spatial context within a single FFPE tissue slide. This project aim was to acquire data-dependent data (DDA) on Exploris 480 to demonstrate the sensitivity of the In-insert protocol sensitivity and benchmark it with intersecting protocol published by Weke et al. (2022).
HostingRepository	PRIDE
AnnounceDate	2024-06-03
AnnouncementXML	Submission_2024-06-03_11:28:50.390.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jakub Faktor
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-24 07:52:39	ID requested
⏵ 1	2024-06-03 11:28:50	announced

Dataset with its publication pending

submitter keyword: Human, limited proteomics, breast tissue, formalin-fixed paraffin-embedded tissue, mammary acini, Exploris 480, laser capture microdissection, spatial proteomics

Sachin Kote
contact affiliation	International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, Gdansk, Poland
contact email	sachin.kote@ug.edu.pl
lab head
Jakub Faktor
contact affiliation	University of Gdansk Kladki 24 Gdansk
contact email	jakub.faktor@ug.edu.pl
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/2024/06/PXD051706

PRIDE project URI

• PRIDE
  1. PXD051706
     1. Label: PRIDE project
     2. Name: Novel protocol for spatial proteome analysis of microdissected formalin-fixed paraffin-embedded tissues