PXD064311

PXD064311 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Retention time calibration for RP-HPLC at pH 9
Description	The change in pH of the mobile phase drastically changes the retention mechanism of peptides, rendering currently available retention time prediction models useless. The aim of this study is to create a dataset of peptide retention times under basic (pH 9) HPLC conditions, allowing for the creation of a retention time prediction model specific for these conditions. Peptides were separated using basic mobile phases and analyzed in positive ion mode, allowing identification with common shotgun proteomics pipeline.
HostingRepository	PRIDE
AnnounceDate	2026-02-13
AnnouncementXML	Submission_2026-02-13_06:44:43.617.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD064311
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Vladimir Gorshkov
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-26 13:35:10	ID requested
⏵ 1	2026-02-13 06:44:44	announced

Publication List

10.6019/PXD064311;
10.1038/s41467-026-68981-5;
Bouwmeester R, Nameni A, Declercq A, Devreese R, Velghe K, Gorshkov V, Penanes PA, Kjeldsen F, Rompais M, Carapito C, Gabriels R, Martens L, Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups. Nat Commun, 17(1):(2026) [pubmed]

10.6019/PXD064311;

10.1038/s41467-026-68981-5;

Bouwmeester R, Nameni A, Declercq A, Devreese R, Velghe K, Gorshkov V, Penanes PA, Kjeldsen F, Rompais M, Carapito C, Gabriels R, Martens L, Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups. Nat Commun, 17(1):(2026) [pubmed]

Keyword List

submitter keyword: HeLa, basic pH, RP-HPLC

submitter keyword: HeLa, basic pH, RP-HPLC

Contact List

Frank Kjeldsen
contact affiliation	Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
contact email	frankk@bmb.sdu.dk
lab head
Vladimir Gorshkov
contact affiliation	University of Southern Denmark
contact email	vgor@bmb.sdu.dk
dataset submitter

Full Dataset Link List

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/2026/02/PXD064311
PRIDE project URI

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/2026/02/PXD064311

PRIDE project URI

Repository Record List

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