Dataset Information

Proteome study to optimize Zeno SWATH DIA

ABSTRACT: 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.

ORGANISM(S): Homo Sapiens (human) Cellular Organisms Mus Musculus (mouse)

SUBMITTER: Sumio Ohtsuki

PROVIDER: PXD050030 | JPOST Repository | Sat Jul 20 00:00:00 BST 2024

REPOSITORIES: jPOST

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Dataset's files

Source:

			Action	DRS
	Optimize_1.9Da_Conventional.scan	Other
	Optimize_1.9Da_Conventional.wiff	Wiff
	Optimize_1.9Da_Conventional.wiff2	Wiff
	Optimize_1.9Da_Method1.scan	Other
	Optimize_1.9Da_Method1.wiff	Wiff

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Publications

Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition.

Gu Kongxin K Kumabe Haruka H Yamamoto Takumi T Tashiro Naoto N Masuda Takeshi T Ito Shingo S Ohtsuki Sumio S

Journal of proteome research 20240709 8

Data-independent acquisition (DIA) techniques such as sequential window acquisition of all theoretical mass spectra (SWATH) acquisition have emerged as the preferred strategies for proteomic analyses. Our study optimized 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 and 2.9 Da) on a ZenoTOF 7600 (Sciex); the acquired data were ...[more]

PMID: 38978496

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