Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition

doi:10.1007/s13361-019-02243-1

	Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition
	Li, Wenxue 1; Chi, Hao 2; Salovska, Barbora 1,3; Wu, Chongde 1; Sun, Liangliang 4; Rosenberger, George 5; Liu, Yansheng 1,6
	2019-08-01
发表期刊	JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
ISSN	1044-0305
卷号	30 期号:8 页码:1396-1405
摘要	Due to the technical advances of mass spectrometers, particularly increased scanning speed and higher MS/MS resolution, the use of data-independent acquisition mass spectrometry (DIA-MS) became more popular, which enables high reproducibility in both proteomic identification and quantification. The current DIA-MS methods normally cover a wide mass range, with the aim to target and identify as many peptides and proteins as possible and therefore frequently generate MS/MS spectra of high complexity. In this report, we assessed the performance and benefits of using small windows with, e.g., 5-m/z width across the peptide elution time. We further devised a new DIA method named RTwinDIA that schedules the small isolation windows in different retention time blocks, taking advantage of the fact that larger peptides are normally eluting later in reversed phase chromatography. We assessed the direct proteomic identification by using shotgun database searching tools such as MaxQuant and pFind, and also Spectronaut with an external comprehensive spectral library of human proteins. We conclude that algorithms like pFind have potential in directly analyzing DIA data acquired with small windows, and that the instrumental time and DIA cycle time, if prioritized to be spent on small windows rather than on covering a broad mass range by large windows, will improve the direct proteome coverage for new biological samples and increase the quantitative precision. These results further provide perspectives for the future convergence between DDA and DIA on faster MS analyzers.
关键词	Data-independent acquisition Isolation windows Maxquant pFind Spectronaut
DOI	10.1007/s13361-019-02243-1
收录类别	SCI
语种	英语
资助项目	Yale Cancer Systems Biology Symposium ; Yale Cancer Center
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry ; Spectroscopy
WOS类目	Biochemical Research Methods ; Chemistry, Analytical ; Chemistry, Physical ; Spectroscopy
WOS记录号	WOS:000478080900008
出版者	SPRINGER
引用统计	被引频次：24[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4540
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Liu, Yansheng
作者单位	1.Yale Univ, Yale Canc Biol Inst, West Haven, CT 06516 USA 2.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China 3.Czech Acad Sci, Inst Mol Genet, Dept Genome Integr, Prague, Czech Republic 4.Michigan State Univ, Dept Chem, E Lansing, MI 48824 USA 5.Columbia Univ, Dept Syst Biol, New York, NY USA 6.Yale Univ, Sch Med, Dept Pharmacol, New Haven, CT 06520 USA
推荐引用方式 GB/T 7714	Li, Wenxue,Chi, Hao,Salovska, Barbora,et al. Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition[J]. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY,2019,30(8):1396-1405.
APA	Li, Wenxue.,Chi, Hao.,Salovska, Barbora.,Wu, Chongde.,Sun, Liangliang.,...&Liu, Yansheng.(2019).Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition.JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY,30(8),1396-1405.
MLA	Li, Wenxue,et al."Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition".JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 30.8(2019):1396-1405.