PXD050030

PXD050030 is an original dataset announced via ProteomeXchange.

Title	Proteome study to optimize Zeno SWATH DIA
Description	Data-independent acquisition (DIA) techniques, such as SWATH acquisition, have emerged as the preferred strategy for proteomic analysis. Our study optimizes the SWATH-DIA method using a narrow isolation window placement approach improving its proteomic performance. We optimized the acquisition parameter combinations of narrow isolation windows with different widths (1.9 Da and 2.9 Da) on a ZenoTOF 7600 (Sciex); the acquired data were analyzed using DIA-NN (version 1.8.1). Narrow SWATH (nSWATH) identified 5,916 and 7,719 protein groups on the digested peptides corresponding to 400 ng of protein from mouse liver and HEK293T cells, improving identification by 7.52% and 4.99%, respectively, compared to that in conventional SWATH. The median coefficient of variation (CV) of the quantified values was less than 6%. We further analyzed benchmark samples comprising peptides from known ratios of E. coli, yeast, and human peptides using nSWATH. Consequently, it achieved accuracy and precision comparable to conventional SWATH, identifying an average of 95,456 precursors and 9,342 protein groups across three benchmark samples, representing 12.6% and 9.63% improved identification compared to conventional SWATH. Furthermore, nSWATH detected lower-abundance proteins than conventional SWATH.
HostingRepository	jPOST
AnnounceDate	2024-07-20
AnnouncementXML	Submission_2024-07-19_08:00:07.930.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sumio Ohtsuki
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: cellular organisms; NCBI TaxID: 131567; scientific name: cellular organisms; NCBI TaxID: 131567;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine
Instrument	instrument; instrument; ZenoTOF 7600

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-22 04:09:36	ID requested
⏵ 1	2024-07-19 08:00:08	announced

Gu K, Kumabe H, Yamamoto T, Tashiro N, Masuda T, Ito S, Ohtsuki S, Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition. J Proteome Res, 23(8):3484-3495(2024) [pubmed]

submitter keyword: data-independent acquisition (DIA), narrow isolation windows, SWATH, parameter optimization, benchmarking

Sumio Ohtsuki
lab head
Sumio Ohtsuki
contact affiliation	Kumamoto University
dataset submitter

jPOST dataset URI

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