PXD017269

PXD017269 is an original dataset announced via ProteomeXchange.

Title	A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis
Description	Formalin fixation and paraffin-embedding (FFPE) is the most common method to preserve human tissue for clinical diagnosis and FFPE archives represent an invaluable resource for biomedical research. Proteins in FFPE material are stable over decades but their efficient extraction and streamlined analysis by mass spectrometry (MS)-based proteomics has so far proven challenging. Here, we describe an MS-based proteomic workflow for quantitative profiling of large FFPE tissue cohorts directly from pathology glass slides. We demonstrate broad applicability of the workflow to clinical pathology specimens and variable sample amounts, including low-input cancer tissue isolated by laser microdissection. Using state-of-the-art data dependent acquisition (DDA) and data independent (DIA) MS workflows, we consistently quantify a large part of the proteome in 100 min single-run analyses. In an adenoma cohort comprising more than 100 samples, total work up took less than a day. We observed a moderate trend towards lower protein identifications in long-term stored samples (>15 years) but clustering into distinct proteomic subtypes was independent of archival time. Our results underline the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and prove the feasibility of analyzing large tissue cohorts in a robust, timely and streamlined manner.
HostingRepository	PRIDE
AnnounceDate	2020-04-02
AnnouncementXML	Submission_2020-04-02_08:47:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fabian Coscia
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-23 06:20:57	ID requested
⏵ 1	2020-04-02 08:47:24	announced

Coscia F, Doll S, Bech JM, Schweizer L, Mund A, Lengyel E, Lindebjerg J, Madsen GI, Moreira JM, Mann M, A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis. J Pathol, 251(1):100-112(2020) [pubmed]

submitter keyword: Proteomics, Biobank, FFPE, Protocol, Cancer, Tissue, Mass spectrometry

Matthias Mann
contact affiliation	Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried
contact email	mmann@biochem.mpg.de
lab head
Fabian Coscia
contact affiliation	University of Copenhagen NNF Center for Protein Research
contact email	fabian.coscia@cpr.ku.dk
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/2020/04/PXD017269

PRIDE project URI

• PRIDE
  1. PXD017269
     1. Label: PRIDE project
     2. Name: A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis