PXD059304

PXD059304 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Two-step peptide solubilization increases coverage in high-sensitivity nanoHILIC/MS/MS-based proteomics
Description	Nanoscale hydrophilic-interaction chromatography coupled with tandem mass spectrometry (nanoHILIC/MS/MS) is a promising alternative to reversed-phase liquid chromatography (RPLC) for proteomics, but its application is limited by the poor solubility of peptides in organic solvent-rich sample solutions. To overcome this issue, we have developed a two-step solubilization method, in which peptides are first solubilized in a solvent with an optimal acetonitrile (ACN) concentration of 25 %, and then diluted into a high ACN concentration solution of 95 %. This procedure increases the peptide solubility without compromising compatibility with nanoHILIC/MS/MS. Compared to direct solubilization in 95 % ACN, this approach increased the intensity of 82.8 % of commonly quantified peptides in nanoHILIC/MS/MS, with an average intensity gain of 20.9 %. Furthermore, nanoHILIC/MS/MS with this two-step solubilization outperformed nanoRPLC/MS/MS, identifying 8.47 times more peptides and 3.54 times more protein groups from 2.5 ng of tryptic peptides extracted from HeLa cells. The high sensitivity of nanoHILIC/MS/MS can be attributed to enhanced loading of peptides as a result of the two-step solubilization, together with superior ESI efficiency arising from the use of the ACN-rich mobile phase. This high-sensitivity proteomics system is a promising platform for clinical and single-cell applications.
HostingRepository	jPOST
AnnounceDate	2025-05-08
AnnouncementXML	Submission_2025-05-07_17:37:48.918.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Koshin Akamatsu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Bos taurus; NCBI TaxID: 9913;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide
Instrument	Orbitrap Exploris 480; Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-29 21:42:05	ID requested
⏵ 1	2025-05-07 17:37:49	announced

Publication List

Akamatsu K, Kanao E, Tomioka A, Ishihama Y, Two-Step Peptide Solubilization Increases Coverage in High-Sensitivity NanoHILIC/MS/MS-Based Proteomics. Anal Chem, 97(19):10227-10235(2025) [pubmed]

Akamatsu K, Kanao E, Tomioka A, Ishihama Y, Two-Step Peptide Solubilization Increases Coverage in High-Sensitivity NanoHILIC/MS/MS-Based Proteomics. Anal Chem, 97(19):10227-10235(2025) [pubmed]

Keyword List

submitter keyword: NanoHILIC/MS/MS

submitter keyword: NanoHILIC/MS/MS

Contact List

Yasushi Ishihama
lab head
Koshin Akamatsu
contact affiliation	Kyoto University
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST dataset 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.jpostdb.org/JPST003452/