Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry
Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry
复制标题
通过所有理论碎片离子质谱的顺序窗口采集来优化采集和数据处理参数，以改进蛋白质组定量。
DOI：
10.1021/acs.jproteome.6b00767
复制
发表时间：
2017-02-01
影响因子：
4.4
通讯作者：
Shui, Wenqing
中科院分区：
文献类型：
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作者：
Li, Shanshan;Cao, Qichen;Shui, Wenqing
近年来，以全理论片段离子谱序列窗口获取（SWATH）技术为代表的数据独立采集（DIA）方法在蛋白质组学分析中获得了广泛的关注，因为DIA能够克服传统数据依赖采集（DDA）方法的固有弱点，并为蛋白质组范围的定量提供更高的全面性和可重复性。尽管原始质谱（MS）数据质量和数据挖掘工作流程可能会影响基于SWATH的蛋白质组学定量的通量、准确性和一致性，但目前还缺乏对SWATH MS分析的采集和数据处理参数的系统评估和优化。在此，我们评估了主要采集参数（如前驱体质量范围、隔离窗宽度和积累时间）以及数据处理变量（包括峰提取标准和谱库选择）对SWATH性能的影响。与大多数SWATH蛋白质组学研究中采用的原始设置相比，微调这些相互依赖的参数可以进一步提高SWATH定量的吞吐量和准确性。此外，我们比较了两种广泛使用的峰提取软件PeakView和Spectronaut在发现生物学背景下差异表达蛋白方面的有效性。我们的工作被认为有助于更深入地了解SWATH MS实验中的关键因素，并帮助研究人员根据样品类型、可用仪器和软件优化SWATH参数和工作流程。
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.