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Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry | |
2017-02 | |
发表期刊 | JOURNAL OF PROTEOME RESEARCH (IF:3.8[JCR-2023],4.1[5-Year]) |
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 | 正在获取...
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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. |
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