PXD056224

PXD056224 is an original dataset announced via ProteomeXchange.

Title	Development of a capillary electrophoresis coupled to mass spectrometry pipeline for comparable assessment of the plasma peptidome
Description	Although capillary electrophoresis coupled to mass spectrometry (CE-MS) holds promise for urinary peptide profiling, only a limited number of studies have used CE-MS to study plasma peptides. Here we describe the establishment of a workflow, including sample preparation, CE-MS and MS/MS analyses, data processing and normalisation optimized for the analysis of plasma peptides. Using 293 plasma samples from 136 patients with end stage kidney failure (including pre- and post-dialysis samples) and 22 patients with chronic kidney disease, we identified and quantified the abundance of 3920 unique plasma peptides. The repeatability and intermediate precision of the analysis were high (with a coefficient of variation of 15% on average for all peptides). 644 out of 3920 peptides were sequenced by CE-MS/MS. These peptide fragments belonged to 129 parent proteins that were also found in Human Plasma PeptideAtlas. Using the pipeline, we identified 188 sequenced plasma peptides with different plasma abundance before and after dialysis. These peptides combined in a support vector machine (SVM) classifier successfully discriminated between pre- and post- dialysis samples in a blinded validation cohort of 45 dialysis patients. Enriched peptides after dialyses were for the major part associated to inflammation. In conclusion, this high-throughput strategy could contribute to address the need for reliable plasma biomarkers of disease.
HostingRepository	PRIDE
AnnounceDate	2025-05-16
AnnouncementXML	Submission_2025-05-16_08:09:59.770.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Carine Froment
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-25 01:16:32	ID requested
⏵ 1	2025-05-16 08:10:00	announced

10.1002/pmic.202400114;

Fernandez L, Breuil B, Froment C, Seye M, Sylla B, Estanco M, Chaubet A, Delecroix E, Chaoui K, Vu JP, Ardeleanu S, Faguer S, Burlet-Schiltz O, Buffin-Meyer B, Schanstra JP, Klein J, Development and Validation of a Capillary Electrophoresis Coupled to Mass Spectrometry Pipeline for Comparable Assessment of the Plasma Peptidome. Proteomics, ():e202400114(2025) [pubmed]

submitter keyword: chronic kidney disease, plasma, cardiovascular diseases, peptidome, biomarkers, CE-MS/MS

Joost-Peter Schanstra
contact affiliation	Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France Université Toulouse III Paul-Sabatier, 31062 Toulouse, France.
contact email	joost-peter.schanstra@inserm.fr
lab head
Carine Froment
contact affiliation	IPBS-CNRS
contact email	carine.froment@ipbs.fr
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/2025/05/PXD056224

PRIDE project URI

• PRIDE
  1. PXD056224
     1. Label: PRIDE project
     2. Name: Development of a capillary electrophoresis coupled to mass spectrometry pipeline for comparable assessment of the plasma peptidome