PXD010328-1

PXD010328 is an original dataset announced via ProteomeXchange.

Title	Identification and validation of stage-associated serum biomarkers in colorectal cancer_discovery phase C
Description	Colorectal cancer (CRC) is one of the most prevalent and lethal cancer diseases worldwide. Here, we aimed to identify and quantify CRC serum biomarkers by combining a robust label-free quantification procedure followed of two consecutive steps of targeted parallel reaction monitoring (PRM) for biomarker validation in a fully inclusive proteomic strategy. For the discovery phase pooled serum samples were used for shotgun proteomics and label-free quantification. On the identification phase, 116 potential biomarkers were selected based on their statistical significance and their relative expression in disease stages respect to healthy stage and their functional relation with cancer progression. Verification phase was conducted in 2 steps. In the first step, 318 peptides from 116 proteins were used for PRM verification giving place to 23 PRM-quantifiable, potential CRC biomarkers. In a second step, 7 peptides corresponding to CO9, APOC3, CRP, THSB1, ECM1 and IGF2 proteins were reproducibly confirmed by PRM in every CRC stage for these unfractionated samples. Finally, a different cohort composed by individual serum samples was used in the final validation phase. In individual serum samples, 5 peptides belonging to 4 proteins were consistently quantified and validated. ROC analyses indicated that peptides GWVTDGFSSLK and LCNNPTPQFGGK were suitable candidates for predicting the separation between control and CRC patients. Two assays for absolute quantification of significant peptides in serum samples were established using AQUA peptides. In conclusion, a set of serum peptides were validated by PRM as potential biomarkers for differentiating control from CRC patients.
HostingRepository	PRIDE
AnnounceDate	2022-03-01
AnnouncementXML	Submission_2022-03-01_11:20:22.308.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	CONSUELO MARIN VICENTE
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-06 01:31:39	ID requested
⏵ 1	2022-03-01 11:20:22	announced
2	2023-11-14 08:49:54	announced	2023-11-14: Updated project metadata.

10.1002/PRCA.201900052;

curator keyword: Biomedical

submitter keyword: colorectal cancer, parallel reaction monitoring, disease biomarkers, diagnosis

José Ignacio Casal Álvarez
contact affiliation	Functional proteomics group; Molecular Biomedicine department; CIB-CSIC
contact email	icasal@cib.csic.es
lab head
CONSUELO MARIN VICENTE
contact affiliation	CIB-CSIC
contact email	cmarin@um.es
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/2022/03/PXD010328

PRIDE project URI

• PRIDE
  1. PXD010328
     1. Label: PRIDE project
     2. Name: Identification and validation of stage-associated serum biomarkers in colorectal cancer_discovery phase C