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

文献类型：期刊论文

作者Li, Wenxue2; Chi, Hao3; Salovska, Barbora2,4; Wu, Chongde2; Sun, Liangliang5; Rosenberger, George1; Liu, Yansheng2,6
刊名JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
出版日期2019-08-01
卷号30期号:8页码:1396-1405
ISSN号1044-0305
关键词Data-independent acquisition Isolation windows Maxquant pFind Spectronaut
DOI10.1007/s13361-019-02243-1
英文摘要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.
资助项目Yale Cancer Systems Biology Symposium ; Yale Cancer Center
WOS研究方向Biochemistry & Molecular Biology ; Chemistry ; Spectroscopy
语种英语
出版者SPRINGER
WOS记录号WOS:000478080900008
源URL[http://119.78.100.204/handle/2XEOYT63/4539]  
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.Columbia Univ, Dept Syst Biol, New York, NY USA
2.Yale Univ, Yale Canc Biol Inst, West Haven, CT 06516 USA
3.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China
4.Czech Acad Sci, Inst Mol Genet, Dept Genome Integr, Prague, Czech Republic
5.Michigan State Univ, Dept Chem, E Lansing, MI 48824 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.

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来源：计算技术研究所

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