PXD029729

PXD029729 is an original dataset announced via ProteomeXchange.

Title	In-depth mass spectrometry-based proteomics of formalin-fixed, paraffin embedded tissues with a spatial resolution of 50–200 µm
Description	Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories as a cost-effective means of preserving invaluable specimens for subsequent study, including for clinical proteomics in translational medicine. With the rapid growth of spatial proteomics, FFPE tissue samples can serve as a more accessible alternative to commonly used fresh frozen tissues. However, extracting proteins from FFPE tissue for analysis by mass spectrometry has been challenging due to crosslinks formed between proteins and formalin, particularly when studying limited samples. We have previously demonstrated that nanoPOTS (Nanodroplet Processing in One Pot for Trace Samples) is an enabling technology for high-resolution and in-depth spatial and single-cell proteomics measurements, but only fresh frozen tissues had been previously analyzed. Here we have adapted the nanoPOTS sample processing workflows for proteome profiling of 10-µm-thick FFPE tissues with lateral dimensions as small as 50 µm. Following a comparison of extraction solvents, times, and temperatures, and under the most favorable conditions, we respectively identified an average of 1180 and 2990 proteins from FFPE preserved mouse liver tissues having dimensions of 50 µm and 200 µm. This was on average 87% of the coverage achieved for fresh frozen mouse liver samples analyzed with the same general procedure. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. These workflows provide the greatest depth of coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:53:51.751.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ryan Kelly
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-12 08:01:10	ID requested
1	2022-08-01 20:01:13	announced
⏵ 2	2023-11-14 08:53:52	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Fresh Frozen, Spatial, DDM,FFPE, LCM

Ryan T Kelly
contact affiliation	Department of Chemistry and Biochemistry, Brigham Young University.
contact email	ryan@chem.byu.edu
lab head
Ryan Kelly
contact affiliation	Brigham Young University
contact email	ryan.kelly@byu.edu
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/2022/08/PXD029729

PRIDE project URI

• PRIDE
  1. PXD029729
     1. Label: PRIDE project
     2. Name: In-depth mass spectrometry-based proteomics of formalin-fixed, paraffin embedded tissues with a spatial resolution of 50–200 µm