Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet
Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet
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DOI：
10.1074/mcp.o114.044917
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发表时间：
2015-05-01
影响因子：
7
通讯作者：
Moritz, Robert L.
中科院分区：
文献类型：
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作者：
Keller, Andrew;Bader, Samuel L.;Moritz, Robert L.
质谱技术的蛋白质组学被广泛用于鉴定和定量肽和蛋白质。肽检测的广度和灵敏度随着数据独立采集质谱的出现而提高。然而，由于碎片离子光谱的复杂性，这些数据的分析是具有挑战性的，所述碎片离子光谱具有来自多个共洗脱前体离子的贡献。我们提出了SWATHProphet软件，该软件可识别和定量独立于数据的采集数据中的肽碎片离子痕迹，提供准确的概率以确保结果正确，并自动检测和去除干扰前体离子对定量的贡献。集成在广泛使用的开源Trans-Proteomic Pipeline中有助于后续分析，例如将多个数据集的结果结合在一起，以使用iProphet提高区分度，并使用ProteinProphet推断样品蛋白质。这一新的发展将大大有助于使大量用户可以使用数据独立的采集质谱法。
Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectrometry. Analysis of such data, however, is challenging due to the complexity of fragment ion spectra that have contributions from multiple co-eluting precursor ions. We present SWATHProphet software that identifies and quantifies peptide fragment ion traces in data-independent acquisition data, provides accurate probabilities to ensure results are correct, and automatically detects and removes contributions to quantitation originating from interfering precursor ions. Integration in the widely used open source Trans-Proteomic Pipeline facilitates subsequent analyses such as combining results of multiple data sets together for improved discrimination using iProphet and inferring sample proteins using ProteinProphet. This novel development should greatly help make data-independent acquisition mass spectrometry accessible to large numbers of users.