PXD051706 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-04-24 07:52:39 | ID requested | |
⏵ 1 | 2024-06-03 11:28:50 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Human, limited proteomics, breast tissue, formalin-fixed paraffin-embedded tissue, mammary acini, Exploris 480, laser capture microdissection, spatial proteomics |
Contact List
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 | |
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/2024/06/PXD051706 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD051706
- Label: PRIDE project
- Name: Novel protocol for spatial proteome analysis of microdissected formalin-fixed paraffin-embedded tissues