PXD013533

PXD013533 is an original dataset announced via ProteomeXchange.

Title	Identification of a collagen marker in urine improves the detection of colorectal liver metastases
Description	Previously, we reported that a combination of a collagen alpha-1(I) natural occurring peptide (NOP) AGPP(-OH)GEAGKP(-OH)GEQGVP(-OH)GDLGAP(-OH)GP (AGP) and serum carcinoembryonic antigen (CEA) has the potential to detect colorectal liver metastases (CRLM). The combined method needs to be adapted to increase the sensitivity and specificity before it can be implemented in the clinic. This mass spectrometry study aimed to identify additional collagen NOPs in urine to further increase the sensitivity and specificity of our previously published method and search for the most discriminating NOP panel. The new assay was developed based on urine samples from 100 healthy controls and 100 patients suffering from CRLM. Two additional NOPs were identified: GPPGEAGK(-OH)P(-OH)GEQGVP(-OH)GDLGAP(-OH)GP (GPP) originating from collagen alpha-1(I) and GNDGARGSDGQPGPP(-OH)GP(-OH)P(-OH)GTAGFP(-OH)GSP(-OH)GAK(-OH)GEVGP (GND) originating from collagen alpha-1(III). A molecular model combining NOPs (AGP, GPP, and GND) and CEA was generated. Molecules that did not contribute to the diagnostic power of the model were removed, resulting in a model only consisting of GND and CEA. In this model, 86% sensitivity and 84% specificity in the discovery set, and 92% sensitivity and 90% specificity in the validation set were reached. These percentages are significantly higher than the current model based on AGP and CEA (p=0.032). The performance of the new model is better than the currently used techniques in the clinic (e.g. CT-scan, ultrasound, serum CEA), which have a sensitivity between 57-70% and a specificity between 90-96%.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:56:17.185.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nick van Huizen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-16 09:03:11	ID requested
1	2019-11-15 01:04:27	announced
⏵ 2	2024-10-22 04:56:17	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.9b00474;

van Huizen NA, van Rosmalen J, Dekker LJM, Coebergh van den Braak RRJ, Verhoef C, IJzermans JNM, Luider TM, Identification of a Collagen Marker in Urine Improves the Detection of Colorectal Liver Metastases. J Proteome Res, 19(1):153-160(2020) [pubmed]

submitter keyword: Logistic regression model, Colon cancer, Colorectal cancer, PRM,Collagen, Colorectal liver metastases, Mass spectrometry, Natural occurring peptides, Urine

Theo M. Luider
contact affiliation	Lab. Neuro-Oncology and Clinical Cancer Proteomics, Erasmus Medical Center, the Netherlands
contact email	t.luider@erasmusmc.nl
lab head
Nick van Huizen
contact affiliation	Erasmus MC
contact email	n.vanhuizen@erasmusmc.nl
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/2019/11/PXD013533

PRIDE project URI

• PRIDE
  1. PXD013533
     1. Label: PRIDE project
     2. Name: Identification of a collagen marker in urine improves the detection of colorectal liver metastases