PXD017906

PXD017906 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of distal cholangiocarcinoma
Description	Distal cholangiocarcinoma is an aggressive malignancy with a dismal prognosis. There is a lack of diagnostic and prognostic biomarkers. An improved understanding of proteomic changes associated with malignancy and identification of potential biomarkers can help improve the survival of patients. A workflow utilizing discovery mass spectrometry and verification by parallel-reaction monitoring was used to analyze surgically resected formalin-fixed paraffin embedded samples from distal cholangiocarcinoma patients and normal bile ducts in order to identify differentially expressed proteins. 20 tumors and 6 controls were successfully analyzed in the discovery experiment and 16 tumors and 9 controls in the PRM analysis. In the discovery experiment a total of 3057 proteins were identified. 87 proteins were found to be differentially expressed between the conditions (q<0.05 and fold change ≥2 or ≤0.5). 31 proteins were upregulated in the distal cholangiocarcinoma samples as compared to controls and 56 downregulated. Bioinformatic analysis revealed an abundance of the differentially expressed proteins to be associated with the tumor reactive stroma. Parallel-reaction monitoring verified 28 proteins as upregulated and 18 as downregulated. In conclusion several proteins without prior association with cholangiocarcinoma biology were identified and verified as differentially expressed between distal cholangiocarcinoma samples and normal bile ducts. These proteins can be further evaluated to elucidate their biomarker potential and role in distal cholangiocarcinoma carcinogenesis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:11:59.894.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Johannes Byrling
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-05 08:24:43	ID requested
1	2020-09-08 23:24:57	announced
⏵ 2	2024-10-22 05:12:00	announced	2024-10-22: Updated project metadata.

Byrling J, Kristl T, Hu D, Pla I, Sanchez A, Sasor A, Andersson R, Marko-Varga G, Andersson B, Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker. J Transl Med, 18(1):343(2020) [pubmed]

10.1186/s12967-020-02498-3;

submitter keyword: PRM,Bile duct cancer, cholangiocarcinoma, LC-MS/MS

Bodil Andersson
contact affiliation	Department of Surgery. Clincal Sciences Lund. Lund University
contact email	bodil.andersson@med.lu.se
lab head
Johannes Byrling
contact affiliation	Lund University Department of Surgery
contact email	johannes.byrling@med.lu.se
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/2020/09/PXD017906

PRIDE project URI

• PRIDE
  1. PXD017906
     1. Label: PRIDE project
     2. Name: Proteomic analysis of distal cholangiocarcinoma