Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry

doi:10.1021/acs.jproteome.6b00767

	Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry
	Li, Shanshan1 ; Cao, Qichen 2; Xiao, Weidi 3; Guo, Yufeng 2; Yang, Yunfei 3; Duan, Xiaoxiao 3; Shui, Wenqing1
	2017-02
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	16 期号:2 页码:738-747
发表状态	已发表
DOI	10.1021/acs.jproteome.6b00767
摘要	Proteomic analysis with data-independent acquisition (DIA) approaches represented by the sequential window acquisition of all theoretical fragment ion spectra (SWATH) technique has gained intense interest in recent years because DIA is able to overcome the intrinsic weakness of conventional data-dependent acquisition (DDA) methods and afford higher throughout and reproducibility for proteome-wide quantification. Although the raw mass spectrometry (MS) data quality and the data-mining workflow conceivably influence the throughput, accuracy and consistency of SWATH-based proteomic quantification, there lacks a systematic evaluation and optimization of the acquisition and data-processing parameters for SWATH MS analysis. Herein, we evaluated the impact of major acquisition parameters such as the precursor mass range, isolation window width and accumulation time as well as the data-processing variables including peak extraction criteria and spectra library selection on SWATH performance. Fine tuning these interdependent parameters can further improve the throughput and accuracy of SWATH quantification compared to the original setting adopted in most SWATH proteomic studies. Furthermore, we compared the effectiveness of two widely used peak extraction software PeakView and Spectronaut in discovery of differentially expressed proteins in a biological context. Our work is believed to contribute to a deeper understanding of the critical factors in SWATH MS experiments and help researchers optimize their SWATH parameters and workflows depending on the sample type, available instrument and software.
关键词	SWATH DIA acquisition parameters data processing spectral library proteomic quantification
收录类别	SCI
语种	英语
资助项目	Key Projects in Tianjin Science & Technology Pillar Program[14ZCZDSY00062]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000393539600035
出版者	AMER CHEMICAL SOC
WOS关键词	DATA-INDEPENDENT ACQUISITION ; SWATH-MS DATA ; SACCHAROMYCES-CEREVISIAE ; PEPTIDE IDENTIFICATION ; TARGETED ANALYSIS ; ASSAY LIBRARIES ; PROTEINS ; DYNAMICS ; SPECTRA ; TANDEM
原始文献类型	Article
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/1520
专题	iHuman研究所_PI研究组_水雯箐组
通讯作者	Cao, Qichen; Shui, Wenqing
作者单位	1.ShanghaiTech Univ, iHuman Inst, Shanghai 201210, Peoples R China 2.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China 3.Nankai Univ, Coll Life Sci, Tianjin 300071, Peoples R China
第一作者单位	iHuman研究所
通讯作者单位	iHuman研究所
第一作者的第一单位	iHuman研究所
推荐引用方式 GB/T 7714	Li, Shanshan,Cao, Qichen,Xiao, Weidi,et al. Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry[J]. JOURNAL OF PROTEOME RESEARCH,2017,16(2):738-747.
APA	Li, Shanshan.,Cao, Qichen.,Xiao, Weidi.,Guo, Yufeng.,Yang, Yunfei.,...&Shui, Wenqing.(2017).Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry.JOURNAL OF PROTEOME RESEARCH,16(2),738-747.
MLA	Li, Shanshan,et al."Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry".JOURNAL OF PROTEOME RESEARCH 16.2(2017):738-747.