PXD001084

PXD001084 is an original dataset announced via ProteomeXchange.

Title	Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors
Description	Purpose: To identify proteins and (molecular/biological) pathways associated with differences between benign and malignant epithelial ovarian tumors. Experimental procedures: Serum of six patients with a serous adenocarcinoma of the ovary was collected before treatment, with a control group consisting of six matched patients with a serous cystadenoma. In addition to the serum, homogeneous regions of cells exhibiting uniform histology were isolated from benign and cancerous tissue by laser microdissection. We subsequently employed label-free liquid chromatography tandem mass spectrometry (LC-MSe) to identify proteins in these serum and tissues samples. Analyses of differential expression between samples were performed using Bioconductor packages and in-house scripts in the statistical software package R. Hierarchical clustering and pathway enrichment analyses were performed, as well as network enrichment and interactome analysis using MetaCore. Results: In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively. The differentially expressed protein sets in serum and tissue largely differed with only 2 proteins in common. MetaCore network analysis, however inferred GCR-alpha and Sp1 as common transcriptional regulators. Interactome analysis highlighted 14-3-3 zeta/delta, 14-3-3 beta/alpha, Alpha-actinin 4, HSP60, and PCBP1 as critical proteins in the tumor proteome signature based on their relative overconnectivity.
HostingRepository	PRIDE
AnnounceDate	2014-10-13
AnnouncementXML	Submission_2014-10-13_03:58:09.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gertjan Kramer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt G2 MS

Revision	Datetime	Status	ChangeLog Entry
0	2014-06-24 06:42:12	ID requested
⏵ 1	2014-10-13 03:58:11	announced

Wegdam W, Argmann CA, Kramer G, Vissers JP, Buist MR, Kenter GG, Aerts JM, Meijer D, Moerland PD, Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors. PLoS One, 9(9):e108046(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: Ovarian Cancer, Serum, Tissue, Label Free Quantitation, All Ions Fragmentation, TOPX peptide quantitation

Johannes M.F.G. Aerts
contact affiliation	Clinical Proteomics Group, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
contact email	j.m.aerts@amc.uva.nl
lab head
Gertjan Kramer
contact affiliation	Proteomics Unit
contact email	gertjan.kramer@embl.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001084
     1. Label: PRIDE project
     2. Name: Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors