PXD021964

PXD021964 is an original dataset announced via ProteomeXchange.

Title	Proteomic workflows for high quality quantitative proteome and PTM analysis of clinically relevant samples from FFPE archives
Description	Well-characterized archival FFPE tissues are of much value for prospective biomarker discovery studies. Protocols that offer high-throughput and good reproducibility are essential in proteomics. Therefore, we developed a workflow implementing efficient paraffin removal and protein extraction from FFPE tissues, followed by digestion using suspension Trapping (S-Trap). The protocol was then combined with isobaric labeling/TMTpro 16plex and applied to lung adenocarcinoma patient samples. In total, 9,585 proteins were quantified, and proteins related to clinical outcome and histopathological subtype were detected. Since acetylation is known to play a major role in cancer development, an on-filter acetylation protocol was developed for studying endogenous lysine acetylation. Our method allows identification and localization of lysine acetylation and quantitative comparison between samples. We identified 1,839 acetylated peptides belonging to 1,339 protein groups and showed that the data obtained from FFPE tissues is in concordance with acetylation data from frozen tissues. In summary, we present a reproducible sample preparation workflow optimized for FFPE tissues that resolves known proteomic-related challenges. We demonstrate compatibility of the S-Trap with TMTpro 16plex labeling. And, for the first time, we prove that it is feasible to study endogenous lysine acetylation stoichiometry in FFPE tissues, contributing to better utility of the existing global tissue archives.
HostingRepository	PRIDE
AnnounceDate	2020-12-18
AnnouncementXML	Submission_2020-12-17_23:32:04.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Magdalena Kuras
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-14 01:33:58	ID requested
⏵ 1	2020-12-17 23:32:05	announced

Kuras M, Woldmar N, Kim Y, Hefner M, Malm J, Moldvay J, D, ö, me B, Fillinger J, Pizzatti L, Gil J, Marko-Varga G, Rezeli M, Proteomic Workflows for High-Quality Quantitative Proteome and Post-Translational Modification Analysis of Clinically Relevant Samples from Formalin-Fixed Paraffin-Embedded Archives. J Proteome Res, 20(1):1027-1039(2021) [pubmed]

submitter keyword: FFPE tissue, suspension Trapping (S-Trap), mass spectrometry, cancer, sample preparation, high-throughput, isobaric labeling (TMT), lung adenocarcinoma, clinical proteomics, lysine acetylation stoichiometry

Gyorgy Marko-Varga
contact affiliation	Department of Clinical Sciences Division of Clinical Protein Science and Imganing
contact email	gyorgymarkovarga@hotmail.com
lab head
Magdalena Kuras
contact affiliation	Lund University
contact email	magdalena.kuras@med.lu.se
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/2020/12/PXD021964

PRIDE project URI

• PRIDE
  1. PXD021964
     1. Label: PRIDE project
     2. Name: Proteomic workflows for high quality quantitative proteome and PTM analysis of clinically relevant samples from FFPE archives