PXD001848

PXD001848 is an original dataset announced via ProteomeXchange.

Title	Global Analysis of Protein Folding Thermodynamics for Disease State Characterization, MCF7 vs MDAMB231
Description	Protein biomarkers can be used to characterize and diagnose disease states such as cancer. They can also serve as therapeutic targets. Current methods for protein biomarker discovery, which generally rely on the large-scale analysis of gene and/or protein expression levels, fail to detect protein biomarkers with disease-related functions and unaltered expression levels. Here we describe the large-scale use of thermodynamic measurements of protein folding and stability for disease state characterization and the discovery of protein biomarkers. Using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique, we assayed ~800 proteins for protein folding and stability changes in three different cell culture models of breast cancer including the MCF-10A, MCF-7, and MDA-MB-231 cell lines. The thermodynamic stability profiles generated here created distinct molecular markers for the three cell lines, and a significant fraction (~45%) of the differentially stabilized proteins did not have altered expression levels. Thus, the protein biomarkers reported here created novel molecular signatures of breast cancer and provided additional insight into the molecular basis of the disease. Our results establish the utility of protein folding and stability measurements for the study of disease processes.
HostingRepository	PRIDE
AnnounceDate	2015-04-10
AnnouncementXML	Submission_2015-04-10_02:56:53.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jagat Adhikari
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; monohydroxylated residue; methylthiolated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-02-26 03:58:23	ID requested
⏵ 1	2015-04-10 02:56:54	announced

Adhikari J, West GM, Fitzgerald MC, Global analysis of protein folding thermodynamics for disease state characterization. J Proteome Res, 14(5):2287-97(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: Mass Spectrometry, SILAC, proteomics, protein folding, chemical denaturation, breast cancer, MCF-7, MDA-MB-231, MCF-10A

Michael C. Fitzgerald
contact affiliation	Departments of Chemistry and Biochemistry Duke University
contact email	michael.c.fitzgerald@duke.edu
lab head
Jagat Adhikari
contact affiliation	Duke University
contact email	ja117@duke.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/2015/04/PXD001848

PRIDE project URI

• PRIDE
  1. PXD001848
     1. Label: PRIDE project
     2. Name: Global Analysis of Protein Folding Thermodynamics for Disease State Characterization, MCF7 vs MDAMB231