PXD017902

PXD017902 is an original dataset announced via ProteomeXchange.

Title	Characterization of the human urine proteome in Prostate Cancer
Description	Prostate cancer (PCa) is one of the most prevalent cancers among men and the fifth leading cause of cancer-related death in men. Currently, PCa suspicion is based on abnormal digital rectal examination and/or raised PSA serum levels, with prostate needle biopsy being required for a definitive diagnosis. Histopathological classification of tumours based on GS grading, cancer staging and PSA levels are used to predict the indolent or aggressive progression of the tumour as well as the likelihood of disease recurrence. These diagnosis and prognosis tools for PCa have revealed limited usefulness, especially PSA testing, which despite organ-specificity is not cancer-specific, being associated with low specificity. In this vein, new markers have been proposed in order to increase the accuracy of PCa detection, most of them proteins. Despite the significant efforts that have been undertaken for discovering other biomarkers for PCa management, few were translated into clinical practice. The simple and non-invasive nature of urine collection along with its proteome stability and storing many secreted proteins of prostate origin, makes the identification of PCa urinary biomarkers an attractive approach. With this in mind, we aimed to compare the urinary proteome profile of PCa patients with non-cancer patients in order to identify non-invasive candidate biomarkers for PCa prediction. To fulfil this task, we followed a shotgun LC-MS/MS approach using an Orbitrap instrument. A combination of two different software packages, MaxQuant and Proteome Discover was used to increase the robustness of analysis and enhance the search for new biomarkers. Proteins quantification was based on a label-free quantification approach (false discovery rate (FDR) 1%). The present dataset was used to disclosure potential markers in PCa management.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:36:20.738.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tânia Lima
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-05 04:36:20	ID requested
1	2022-05-19 06:55:29	announced
⏵ 2	2024-10-22 05:36:21	announced	2024-10-22: Updated project metadata.

10.3390/cancers14082001;

Lima T, Barros AS, Trindade F, Ferreira R, Leite-Moreira A, Barros-Silva D, Jer, ó, nimo C, Ara, ú, jo L, Henrique R, Vitorino R, Fardilha M, Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study. Cancers (Basel), 14(8):(2022) [pubmed]

submitter keyword: human

proteome

urine

prostate cancer

Rui Vitorino
contact affiliation	Department of Medical Sciences, Institute of Biomedicine-iBiMED,Univerity of Aveiro, 3810-193 Aveiro,Portugal
contact email	rvitorino@ua.pt
lab head
Tânia Lima
contact affiliation	University of Aveiro
contact email	tanialima@ua.pt
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/2022/05/PXD017902

PRIDE project URI

• PRIDE
  1. PXD017902
     1. Label: PRIDE project
     2. Name: Characterization of the human urine proteome in Prostate Cancer