PXD019924

PXD019924 is an original dataset announced via ProteomeXchange.

Title	Biomarkers of Cholangiocarcinoma and Pancreatic adenocarcinoma
Description	Cholangiocarcinoma (CCA) and pancreatic adenocarcinoma (PDAC) may lead to the development of extrahepatic obstructive cholestasis. However, biliary stenoses can also be caused by benign conditions, and the identification of their etiology still remains a clinical challenge. We performed metabolomic and proteomic analyses of bile from patients with benign (n=36) and malignant conditions, CCA (n=36) or PDAC (n=57), undergoing endoscopic retrograde cholangiopancreatography with the aim of characterizing bile composition in biliopancreatic disease and identifying biomarkers for the differential diagnosis of biliary strictures. Comprehensive analyses of lipids, bile acids and small molecules were carried out using mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (1H-NMR) in all patients. MS analysis of bile proteome was performed in five patients per group. We implemented artificial intelligence tools for the selection of biomarkers and algorithms with predictive capacity. Our machine-learning pipeline included the generation of synthetic data with properties of real data, the selection of potential biomarkers (metabolites or proteins) and their analysis with neural networks (NN). Selected biomarkers were then validated with real data. We identified panels of lipids (n=10) and proteins (n=5) that when analyzed with NN algorithms discriminated between patients with and without cancer with an unprecedented accuracy.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_07:19:32.084.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019924
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Antonio Ramos Fernández
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue; 2-pyrrolidone-5-carboxylic acid (Glu); 2-pyrrolidone-5-carboxylic acid (Gln); acetylated residue; monohydroxylated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-21 23:43:12	ID requested
⏵ 1	2021-09-09 07:19:32	announced

Urman JM, Herranz JM, Uriarte I, Rull, á, n M, Oy, ó, n D, Gonz, á, lez B, Fernandez-Uri, é, n I, Carrascosa J, Bolado F, Zabalza L, Arechederra M, Alvarez-Sola G, Colyn L, Latasa MU, Puchades-Carrasco L, Pineda-Lucena A, Iraburu MJ, Iruarrizaga-Lejarreta M, Alonso C, Sangro B, Purroy A, Gil I, Carmona L, Cubero FJ, Mart, í, nez-Chantar ML, Banales JM, Romero MR, Macias RIR, Monte MJ, Mar, í, n JJG, Vila JJ, Corrales FJ, Berasain C, Fern, á, ndez-Barrena MG, Avila MA, Pilot Multi-Omic Analysis of Human Bile from Benign and Malignant Biliary Strictures: A Machine-Learning Approach. Cancers (Basel), 12(6):(2020) [pubmed]

submitter keyword: Human bile

cholangiocarcinoma

pancreatic adenocarcinoma

lipidomics

proteomics

machine learning

Fernando J. Corrales
contact affiliation	Professor of Biochemistry Proteomics Unit Centro Nacional de Biotecnología (CSIC) Darwin 3, 28049, Madrid
contact email	fcorrales@cnb.csic.es
lab head
Antonio Ramos Fernández
contact affiliation	Proteobotics S.L.
contact email	aramos@proteobotics.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/2021/09/PXD019924

PRIDE project URI

• PRIDE
  1. PXD019924
     1. Label: PRIDE project
     2. Name: Biomarkers of Cholangiocarcinoma and Pancreatic adenocarcinoma