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Optimization of data-independent acquisition-MS for deep proteome analysis

ABSTRACT: Data-independent acquisition (DIA)-MS analysis overtops the existing data-dependent acquisition (DDA)-MS analysis enabling deep proteome coverage and precise relative quantitative analysis in single-shot LC-MS/MS. We constructed a single-shot LC-MS/MS system with an MS measurement time of 90 min for a highly sensitive and deep proteomic analysis by optimizing the parameters of DIA and nanoLC. Furthermore, we applied this system to the proteomic analysis of cerebrums in germ-free and specific pathogen-free mice.

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

SUBMITTER: Yusuke Kawashima

PROVIDER: PXD016032 | JPOST Repository | Mon Oct 28 00:00:00 GMT 2019

REPOSITORIES: jPOST

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			Action	DRS
	90min_DDA_HEK293_200ng_1.raw	Raw
	90min_DDA_HEK293_200ng_2.raw	Raw
	90min_DDA_HEK293_200ng_3.raw	Raw
	90min_GPF1_OverlappingWindowDIA_Cerebrum_Pool_For_library.raw	Raw
	90min_GPF2_OverlappingWindowDIA_Cerebrum_Pool_For_library.raw	Raw

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Publications

Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis.

Kawashima Yusuke Y Watanabe Eiichiro E Umeyama Taichi T Nakajima Daisuke D Hattori Masahira M Honda Kenya K Ohara Osamu O

International journal of molecular sciences 20191126 23

Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteomic analysis overtop the existing data-dependent acquisition (DDA)-MS-based proteomic analysis to enable deep proteome coverage and precise relative quantitative analysis in single-shot liquid chromatography (LC)-MS/MS. However, DIA-MS-based proteomic analysis has not yet been optimized in terms of system robustness and throughput, particularly for its practical applications. We established a single-shot LC-MS/MS system with a ...[more]

PMID: 31779068

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