PXD007962

PXD007962 is an original dataset announced via ProteomeXchange.

Title	Discovery and validation of novel protein biomarkers in ovarian cancer patient urine
Description	Diagnosis of ovarian cancer at an early stage is the most important determinant of survival. Thus, there is a clear need for novel biomarkers to improve diagnostic and prognostics that may better inform on therapeutic strategies. We have conducted a discovery study using label-free quantitative mass spectrometry (LFQ) to identify potential biomarker candidates in urine from individual ovarian cancer patients. LFQ analyses identified 4394 proteins (16397 peptides) in urine samples (n=20), 23 of which were significantly elevated in the malignant patient group compared to patients with benign disease. To validate these changes, we used Parallel Reaction Monitoring (PRM) to investigate their abundance in an independent cohort (n=20) of patient urine samples. Seven of the ten proteins were significantly enriched in the ovarian cancer patient samples; amongst these were established ovarian cancer markers WFDC2 (HE4) and Mesothelin (MSLN), validating our approach. This is the first application of a LFQ-PRM workflow to identify and validate ovarian cancer-specific biomarkers in urine samples.
HostingRepository	PRIDE
AnnounceDate	2018-02-15
AnnouncementXML	Submission_2018-02-15_01:25:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jarrod Sandow
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-13 02:41:55	ID requested
⏵ 1	2018-02-15 01:25:09	announced

Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN, Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine. Proteomics Clin Appl, 12(3):e1700135(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: label free quantitation, LFQ, parallel reaction monitoring, PRM, ovarian cancer, urine, HE4

Andrew Ian Webb
contact affiliation	Systems Biology and Personalised Medicine, Walter & Eliza Hall Institute
contact email	webb@wehi.edu.au
lab head
Jarrod Sandow
contact affiliation	WEHI
contact email	sandow@wehi.edu.au
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/2018/02/PXD007962

PRIDE project URI

• PRIDE
  1. PXD007962
     1. Label: PRIDE project
     2. Name: Discovery and validation of novel protein biomarkers in ovarian cancer patient urine