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PXD056224

PXD056224 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDevelopment of a capillary electrophoresis coupled to mass spectrometry pipeline for comparable assessment of the plasma peptidome
DescriptionAlthough 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.
HostingRepositoryPRIDE
AnnounceDate2025-05-16
AnnouncementXMLSubmission_2025-05-16_08:09:59.770.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterCarine Froment
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-09-25 01:16:32ID requested
12025-05-16 08:10:00announced
Publication List
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]
Keyword List
submitter keyword: chronic kidney disease, plasma, cardiovascular diseases, peptidome, biomarkers, CE-MS/MS
Contact List
Joost-Peter Schanstra
contact affiliationInstitut 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 emailjoost-peter.schanstra@inserm.fr
lab head
Carine Froment
contact affiliationIPBS-CNRS
contact emailcarine.froment@ipbs.fr
dataset submitter
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Dataset FTP location
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