PXD007088

PXD007088 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiles of FFPE breast normal and tumor tissue
Description	Accessing the proteome of formalin fixed, paraffin-embedded (FFPE) tissue could lead to discovery of new biomarkers and development of clinically useful assays. A critical step to realizing this potential is developing a simple and reproducible method to obtain proteomic profiles from FFPE tissue. An objective of this work is to develop and optimize a method to obtain proteomic profiles from FFPE breast tissue using a protocol commonly applied in pathology laboratories. The outcome is a method that incorporates steps used for immunohistochemical analyses of FFPE tissue that results in highly reproducible proteomic profiles. Implementing this assay with normal breast tissue and breast tumor tissue produced proteome profiles that reproducibly demonstrate substantial differences between normal vs. tumor tissue.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:09:17.828.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ten-Yang Yen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Methyl; Oxidation
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-20 05:22:13	ID requested
1	2020-07-16 18:06:55	announced
⏵ 2	2024-10-22 05:09:19	announced	2024-10-22: Updated project metadata.

10.1002/pmic.202000044;

Yen TY, Wong R, Pizzo D, Thein M, Macher BA, Timpe LC, Over-Expression of RNA Processing, Heat Shock, and DNA Repair Proteins in Breast Tumor Compared to Normal Tissue. Proteomics, 20(15-16):e2000044(2020) [pubmed]

ProteomeXchange project tag: Cancer (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Biomedical

submitter keyword: Human, Breast, Protein Profile, FFPE, Tissue, LC-MS/MS

Robert Yen
contact affiliation	Mass Spectrometry Facility, Department of Chemistry and Biochemistry, San Francisco State University, USA
contact email	ryen@sfsu.edu
lab head
Ten-Yang Yen
contact affiliation	San Francisco State University-USA
contact email	ryen@sfsu.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/2020/07/PXD007088

PRIDE project URI

• PRIDE
  1. PXD007088
     1. Label: PRIDE project
     2. Name: Proteomic profiles of FFPE breast normal and tumor tissue