PXD061613

PXD061613 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Validation of Thin-diaPASEF for maximizing proteome coverage
Description	We optimized the parameters of CCS range, polygon scan region, ramp time, and isolation window width to achieve high-depth proteome analysis using the timsTOF HT. As a result, we developed Thin-diaPASEF, which was optimized with a CCS range of 0.7–1.3, a ramp time of 150 ms, an isolation window width of 26 Th (with an overlap width of 1 Th), and a polygon area focused on regions where precursors accumulate. Thin-diaPASEF was then compared with existing methods, including py-diAID PASEF, slice-PASEF, and synchro-PASEF. The results demonstrated that Thin-diaPASEF achieved superior protein identification. Performance evaluation of Thin-diaPASEF revealed the identification of approximately 9,400 proteins with a sample injection of 500 ng and an analysis time of 100 min. Finally, we applied Thin-diaPASEF to plasma proteome analysis. We compared three sample preparation methods: an improved LEL method based on our previously reported plasma and serum preparation approach, Seer’s nanoparticle-based method, and the conventional Top14 column-based method. As a result, the improved LEL method successfully identified 5,378 proteins at an analysis throughput of 24 samples per day.
HostingRepository	jPOST
AnnounceDate	2025-08-10
AnnouncementXML	Submission_2025-08-10_00:14:43.974.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ryo Konno
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: cellular organisms; NCBI TaxID: 131567;
ModificationList	S-carboxamidomethyl-L-cysteine; unknown modification
Instrument	timsTOF HT

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-09 05:42:55	ID requested
⏵ 1	2025-08-10 00:14:44	announced

Publication List

Konno R, Ishikawa M, Nakajima D, Inukai K, Ohara O, Kawashima Y, Thin-diaPASEF: diaPASEF for maximizing proteome coverage in single-shot proteomics. DNA Res, 32(4):(2025) [pubmed]

Konno R, Ishikawa M, Nakajima D, Inukai K, Ohara O, Kawashima Y, Thin-diaPASEF: diaPASEF for maximizing proteome coverage in single-shot proteomics. DNA Res, 32(4):(2025) [pubmed]

Keyword List

submitter keyword: Thin-diaPASEF, single-shot proteomics, diaPASEF, synchro-PASEF, slice-PASEF

submitter keyword: Thin-diaPASEF, single-shot proteomics, diaPASEF, synchro-PASEF, slice-PASEF

Contact List

Yusuke Kawashima
lab head
Ryo Konno
contact affiliation	Kazusa DNA Research Institute.
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/JPST003679/