PXD031946

PXD031946 is an original dataset announced via ProteomeXchange.

Title	A non-hazardous deparaffinization protocol enables quantita-tive proteomics of core needle biopsy-sized formalin-fixed and paraffin embedded (FFPE) tissue specimens.
Description	Most human tumor tissues that are obtained for pathology and diagnostic purposes are forma-lin-fixed and paraffin embedded (FFPE). To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to prote-olytic digestion. A central component of almost all deparaffinization protocols is xylene, a toxic and highly flammable solvent that has been reported to negatively affect protein extraction and quantitative proteome analysis. Here, we present a ‘green’ xylene-free protocol for accel-erated sample preparation of FFPE tissues based on paraffin-removal with hot water. Com-bined with tissue homogenization using disposable micropestles and a modified protein aggre-gation capture (PAC) digestion protocol, our workflow enables streamlined and reproducible quantitative proteomic profiling of FFPE tissue. Label free quantitation of FFPE cores from human ductal breast carcinoma in-situ (DCIS) xenografts with a volume of only 0.79 mm3 showed a high correlation between replicates (r2=0.992) with a median %CV of 16.9%. Im-portantly, this small volume is amenable to tissue micro array (TMA) cores and core needle bi-opsies, while our results and the easy-of-use indicate that a further downsizing is feasible. Fi-nally, our FFPE workflow does not require costly equipment and can be established in every standard clinical laboratory.
HostingRepository	PRIDE
AnnounceDate	2022-05-19
AnnouncementXML	Submission_2022-05-19_04:13:23.851.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Georgia Mitsa
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-28 12:17:20	ID requested
⏵ 1	2022-05-19 04:13:24	announced

Mitsa G, Guo Q, Goncalves C, Preston SEJ, Lacasse V, Aguilar-Mahecha A, Benlimame N, Basik M, Spatz A, Batist G, Miller WH, Del Rincon SV, Zahedi RP, Borchers CH, A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens. Int J Mol Sci, 23(8):(2022) [pubmed]

submitter keyword: Clinical proteomics

tumor tissues

FFPE

quantitative proteomics

core needle biopsy

cancer research

molecular pathology

breast ductal carcinoma

in-situ cancer

Christoph H Borchers
contact affiliation	1.Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada 2.Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec
contact email	christoph.borchers@mcgill.ca
lab head
Georgia Mitsa
contact affiliation	McGill University, Segal Cancer Proteomics Centre
contact email	georgia.mitsa@outlook.com
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/2022/05/PXD031946

PRIDE project URI

• PRIDE
  1. PXD031946
     1. Label: PRIDE project
     2. Name: A non-hazardous deparaffinization protocol enables quantita-tive proteomics of core needle biopsy-sized formalin-fixed and paraffin embedded (FFPE) tissue specimens.