PXD046530

PXD046530 is an original dataset announced via ProteomeXchange.

Title	Multi-omic diagnostics of prostate cancer in the presence of benign prostatic hyperplasia
Description	There is an unmet need for improved diagnostic testing and risk prediction for cases of prostate cancer (PCa) to improve care and reduce overtreatment of indolent disease. Here we have analysed the serum proteome and lipidome of 262 study participants by liquid chromatography-mass spectrometry, including participants with a diagnosis of PCa, benign prostatic hyperplasia (BPH), or otherwise healthy volunteers, with the aim of improving biomarker specificity. Although a two-class machine learning model was able to separate PCa from controls with sensitivity of 0.82 and specificity of 0.95, adding BPH resulted in a statistically significant decline in specificity for prostate cancer to 0.76, with half of BPH cases being misclassified by the model as PCa. A small number of biomarkers differentiating between BPH and prostate cancer were identified, including proteins in MAP Kinase pathways, as well as in lipids containing oleic acid; these may offer a route to greater specificity. These results highlight, however, that whilst there are opportunities for machine learning, these will only be achieved by use of appropriate training sets that include confounding comorbidities, especially when calculating the specificity of a test.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:25:47.957.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lee Gethings
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-31 06:03:18	ID requested
1	2024-01-26 06:58:18	announced
⏵ 2	2024-10-22 06:25:51	announced	2024-10-22: Updated project metadata.

Spick M, Muazzam A, Pandha H, Michael A, Gethings LA, Hughes CJ, Munjoma N, Plumb RS, Wilson ID, Whetton AD, Townsend PA, Geifman N, Multi-omic diagnostics of prostate cancer in the presence of benign prostatic hyperplasia. Heliyon, 9(12):e22604(2023) [pubmed]

10.1016/j.heliyon.2023.e22604;

submitter keyword: Ion Mobility, DIA,Prostate Cancer, Multi-OMICS

Lee Gethings
contact affiliation	Waters Corporation
contact email	lee_gethings@waters.com
lab head
Lee Gethings
contact affiliation	Waters Corporation
contact email	lee_gethings@waters.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/2024/01/PXD046530

PRIDE project URI

• PRIDE
  1. PXD046530
     1. Label: PRIDE project
     2. Name: Multi-omic diagnostics of prostate cancer in the presence of benign prostatic hyperplasia