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
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出版日期 | 2019-08-01 |
卷号 | 30期号:8页码:1396-1405 |
关键词 | Data-independent acquisition Isolation windows Maxquant pFind Spectronaut |
ISSN号 | 1044-0305 |
DOI | 10.1007/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 |
WOS记录号 | WOS:000478080900008 |
出版者 | SPRINGER |
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. |
入库方式: OAI收割
来源:计算技术研究所
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