PXD001034

PXD001034 is an original dataset announced via ProteomeXchange.

Title	Biomarkers for Cervical Cancer. iTRAQ Discovery.
Description	We developed a discovery-validation mass-spectrometry based pipeline to identify a set of proteins that are regulated in serum of patients with cervical intraepithelial neoplasia (CIN) and squamous cell cervical cancer using isobaric Tags for Relative and Absolute Quantitation (iTRAQ®), label-free shotgun and targeted mass-spectrometric quantification. At the discovery stage we used a “pooling” strategy for the comparative analysis of immunodepleted serum from patients with early-(CES) and late-stage (CLS) cervical cancer versus healthy controls that revealed 15 up- and 26 down-regulated proteins. The analysis of a new of non-depleted serum samples from patients with CIN, CES, CLS, and healthy controls showed significant changes in abundance of alpha-1-acid glycoprotein 1, alpha-1-antitrypsin, serotransferrin, haptoglobin, alpha-2-HS-glycoprotein and vitamin D-binding protein. To further validate our findings we developed a fast UPLC/MRM method for the simultaneous targeted quantification of these proteins in a new set of 48 CIN, 50 CES, 34 CLS and 48 healthy controls as well as 49 serum samples from patients with ovarian cancer. The panel of six proteins showed 62% sensitivity and 82 % specificity for discrimination of patients with CIN grade 2 or worse from healthy controls, a stage of the disease where current protein-based biomarkers fail to show any discrimination.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_03:58:10.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001034
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Boichenko
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Phospho; Acetyl; Carbamidomethyl
Instrument	Agilent instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2014-06-04 08:19:37	ID requested
1	2014-10-06 03:14:14	announced
⏵ 2	2014-10-23 03:58:11	announced	Updated project metadata.

Boichenko AP, Govorukhina N, Klip HG, van der Zee AG, G, ü, zel C, Luider TM, Bischoff R, A panel of regulated proteins in serum from patients with cervical intraepithelial neoplasia and cervical cancer. J Proteome Res, 13(11):4995-5007(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: cervical cancer, intraepithelial neoplasia, protein panel, LC-MS/MS, alpha-1-antitrypsin, alpha-1-acid-glycoprotein, haptoglobin, serotransferrin, vitamin D-binding protein, alpha-2-HS-glycoprotein

Rainer Bischoff
contact affiliation	Head of Analytical Biochemistry, University of Groningen
contact email	r.p.h.bischoff@rug.nl
lab head
Alexander Boichenko
contact affiliation	University of Groningen
contact email	oleksandr.boychenko@gmail.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/2014/10/PXD001034

PRIDE project URI

• PRIDE
  1. PXD001034
     1. Label: PRIDE project
     2. Name: Biomarkers for Cervical Cancer. iTRAQ Discovery.