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PXD019924

PXD019924 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBiomarkers of Cholangiocarcinoma and Pancreatic adenocarcinoma
DescriptionCholangiocarcinoma (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.
HostingRepositoryPRIDE
AnnounceDate2021-09-09
AnnouncementXMLSubmission_2021-09-09_07:19:32.084.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD019924
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterAntonio Ramos Fernández
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmethylthiolated residue; 2-pyrrolidone-5-carboxylic acid (Glu); 2-pyrrolidone-5-carboxylic acid (Gln); acetylated residue; monohydroxylated residue
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-06-21 23:43:12ID requested
12021-09-09 07:19:32announced
Publication List
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]
Keyword List
submitter keyword: Human bile
cholangiocarcinoma
pancreatic adenocarcinoma
lipidomics
proteomics
machine learning
Contact List
Fernando J. Corrales
contact affiliationProfessor of Biochemistry Proteomics Unit Centro Nacional de Biotecnología (CSIC) Darwin 3, 28049, Madrid
contact emailfcorrales@cnb.csic.es
lab head
Antonio Ramos Fernández
contact affiliationProteobotics S.L.
contact emailaramos@proteobotics.com
dataset submitter
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Dataset FTP location
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