Krisp Christoph, Molloy Mark P
Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility (APAF), Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia.
Methods Mol Biol. 2017;1619:373-383. doi: 10.1007/978-1-4939-7057-5_25.
The limitations commonly observed in data-dependent acquisition (DDA) mass spectrometric investigation of non-depleted human plasma are mainly due to the large dynamic concentration range of protein expression. Less abundant proteins are usually masked by highly abundant proteins and are therefore difficult to reliably detect. Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) mass spectrometry (MS), as a representative of data-independent acquisition (DIA) approaches, provides an opportunity to improve plasma-based biomarker discovery studies because this approach does not rely on precursor intensity for fragmentation selection but rather analyzes all precursors in specified mass ranges. Here, we describe a workflow for SWATH-MS-based analysis of non-depleted plasma including sample preparation, data acquisition, and statistical analysis.
在对未耗尽的人血浆进行数据依赖型采集（DDA）质谱研究中常见的局限性主要归因于蛋白质表达的动态浓度范围较大。丰度较低的蛋白质通常会被高丰度蛋白质掩盖，因此难以可靠地检测到。作为数据非依赖型采集（DIA）方法的代表，所有理论碎片离子光谱的顺序窗口采集（SWATH）质谱法（MS）为改进基于血浆的生物标志物发现研究提供了一个机会，因为这种方法不依赖于前体强度进行碎片选择，而是分析指定质量范围内的所有前体。在此，我们描述了一种基于SWATH-MS的未耗尽血浆分析工作流程，包括样品制备、数据采集和统计分析。
