PXD024800

PXD024800 is an original dataset announced via ProteomeXchange.

Title	Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories
Description	In this study, we evaluated the feasibility of proteomics and phosphoproteomics on formalin-fixed paraffin-embedded (FFPE) lung tissue for protein extraction protocols, quantification methods, pre-analytics, and sample size. First, we compared three protocols for the extraction of proteins from FFPE tissues and used the best-performing protocol to acquire a deep proteome of lung adenocarcinoma and squamous cell carcinoma. We quantified >8,000 proteins and >14,000 phosphosites with a tandem mass tag (TMT11) approach and 6,700 proteins and 7,000 phosphosites with a microscaled TMT approach, enabling the analysis of FFPE needle biopsies with limited amounts of tissue. This is a considerable increase in coverage compared to label-free quantification techniques. We also evaluated pre-analytical variables such as the influence of fixation times and the duration of heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. We also present general guidelines to what proteomics and phosphoproteomics methods are best suited for different applications for retrospective cancer studies.
HostingRepository	PRIDE
AnnounceDate	2021-05-05
AnnouncementXML	Submission_2021-07-20_00:42:20.181.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Corinna Friedrich
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	2021-03-17 11:14:29	ID requested
1	2021-05-05 10:50:42	announced
⏵ 2	2021-07-20 00:42:20	announced	2021-07-20: Updated publication reference for PubMed record(s): 34117251.

Friedrich C, Schallenberg S, Kirchner M, Ziehm M, Niquet S, Haji M, Beier C, Neudecker J, Klauschen F, Mertins P, Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories. Nat Commun, 12(1):3576(2021) [pubmed]

submitter keyword: FFPE, proteomics, NSCLC

Philipp Mertins
contact affiliation	MDC Berlin
contact email	philipp.mertins@mdc-berlin.de
lab head
Corinna Friedrich
contact affiliation	DKFZ Heidelberg
contact email	corinna.friedrich@dkfz-heidelberg.de
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/2021/05/PXD024800

PRIDE project URI

• PRIDE
  1. PXD024800
     1. Label: PRIDE project
     2. Name: Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories