Synergistic optimization of Liquid Chromatography and Mass Spectrometry parameters on Orbitrap Tribrid mass spectrometer for high efficient data-dependent proteomics

doi:10.1002/jms.4653

	Synergistic optimization of Liquid Chromatography and Mass Spectrometry parameters on Orbitrap Tribrid mass spectrometer for high efficient data-dependent proteomics
	Huang, Peiwu 1,2; Liu, Chao 3,4,5; Gao, Weina 1; Chu, Bizhu 1; Cai, Zongwei 2; Tian, Ruijun 1,6
	2020-09-13
发表期刊	JOURNAL OF MASS SPECTROMETRY
ISSN	1076-5174
页码	10
摘要	Steady improvement in Orbitrap-based mass spectrometry (MS) technologies has greatly advanced the peptide sequencing speed and depth. In-depth analysis of the performance of state-of-the-art MS and optimization of key parameters can improve sequencing efficiency. In this study, we first systematically compared the performance of two popular data-dependent acquisition approaches, with Orbitrap as the first-stage (MS1) mass analyzer and the same Orbitrap (high-high approach) or ion trap (high-low approach) as the second-stage (MS2) mass analyzer, on the Orbitrap Fusion mass spectrometer. High-high approach outperformed high-low approach in terms of better saturation of the scan cycle and higher MS2 identification rate. However, regardless of the acquisition method, there are still more than 60% of peptide features untargeted for MS2 scan. We then systematically optimized the MS parameters using the high-high approach. Increasing the isolation window in the high-high approach could facilitate faster scan speed, but decreased MS2 identification rate. On the contrary, increasing the injection time of MS2 scan could increase identification rate but decrease scan speed and the number of identified MS2 spectra. Dynamic exclusion time should be set properly according to the chromatography peak width. Furthermore, we found that the Orbitrap analyzer, rather than the analytical column, was easily saturated with higher loading amount, thus limited the dynamic range of MS1-based quantification. By using optimized parameters, 10 000 proteins and 110 000 unique peptides were identified by using 20 h of effective liquid chromatography (LC) gradient time. The study therefore illustrated the importance of synchronizing LC-MS precursor ion targeting, fragment ion detection, and chromatographic separation for high efficient data-dependent proteomics.
关键词	chromatography data-dependent acquisition label-free proteomics mass spectrometry precursor determination algorithm
DOI	10.1002/jms.4653
收录类别	SCI
语种	英语
资助项目	Shenzhen Innovation of Science and Technology Commission[JCYJ20170412154126026] ; Guangdong Provincial Natural Science[2016A030312016] ; Guangdong Provincial Fund for Distinguished Young Scholars[2019B151502050] ; China State Key Basic Research Program[2016YFA0501403] ; China State Key Basic Research Program[2016YFA0501404] ; National Natural Science Foundation of China[31700088]
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry ; Spectroscopy
WOS类目	Biochemical Research Methods ; Chemistry, Analytical ; Spectroscopy
WOS记录号	WOS:000568712400001
出版者	WILEY
引用统计	被引频次：9[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/2XEOYT63/15527
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Tian, Ruijun
作者单位	1.Southern Univ Sci & Technol, Dept Chem, Shenzhen 518055, Peoples R China 2.Hong Kong Baptist Univ, Dept Chem, State Key Lab Environm & Biol Anal, Hong Kong, Hong Kong, Peoples R China 3.Beihang Univ, Beijing Adv Innovat Ctr Big Data Based Precis Med, Sch Med & Engn, Beijing 100191, Peoples R China 4.Beihang Univ, Key Lab Big Data Based Precis Med, Minist Ind & Informat Technol, Beijing, Peoples R China 5.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 6.Southern Univ Sci & Technol, Guangdong Prov Key Lab Cell Microenvironm & Dis R, Shenzhen 518055, Peoples R China
推荐引用方式 GB/T 7714	Huang, Peiwu,Liu, Chao,Gao, Weina,et al. Synergistic optimization of Liquid Chromatography and Mass Spectrometry parameters on Orbitrap Tribrid mass spectrometer for high efficient data-dependent proteomics[J]. JOURNAL OF MASS SPECTROMETRY,2020:10.
APA	Huang, Peiwu,Liu, Chao,Gao, Weina,Chu, Bizhu,Cai, Zongwei,&Tian, Ruijun.(2020).Synergistic optimization of Liquid Chromatography and Mass Spectrometry parameters on Orbitrap Tribrid mass spectrometer for high efficient data-dependent proteomics.JOURNAL OF MASS SPECTROMETRY,10.
MLA	Huang, Peiwu,et al."Synergistic optimization of Liquid Chromatography and Mass Spectrometry parameters on Orbitrap Tribrid mass spectrometer for high efficient data-dependent proteomics".JOURNAL OF MASS SPECTROMETRY (2020):10.