Yonsei Proteome Research Center , Seoul 03722, Korea.
J Proteome Res. 2017 Dec 1;16(12):4435-4445. doi: 10.1021/acs.jproteome.6b01019. Epub 2017 Apr 4.
Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.
质谱（MS）是一种广泛应用于生物医学科学的蛋白质组分析工具。在基于 MS 的自上而下的蛋白质鉴定蛋白质组学方法中，由于其简单方便，因此通常使用序列数据库（DB）搜索。但是，使用具有多种可变修饰选项的序列 DB 进行搜索会增加处理时间，并在大型复杂的 MS 数据集上产生假阳性错误。光谱库搜索是一种替代解决方案，可避免序列 DB 搜索的限制，并允许以高灵敏度检测更多肽。不幸的是，该技术的蛋白质组覆盖率较低，从而限制了在生物样品中检测新型和完整肽序列。为了解决这些问题，我们之前开发了“Combo-Spec Search”方法，该方法使用手动的多个参考和模拟光谱库搜索来分析生物样品中的整个蛋白质组。在这项研究中，我们开发了一种新的分析界面工具，称为“Epsilon-Q”，以增强 Combo-Spec Search 方法和无标签蛋白质定量的功能。Epsilon-Q 自动执行多个光谱库搜索，特定类别的错误发现率控制以及结果集成。它具有用户友好的图形界面，并通过支持标准 MS 数据格式和由 SpectraST 提供的谱对谱匹配，在识别和定量蛋白质方面表现出良好的性能。此外，当将 Epsilon-Q 界面与 Combo-Spec 搜索方法（称为 Epsilon-Q 系统）结合使用时，它通过在识别和定量生物样品中的低丰度蛋白质方面优于其他序列 DB 搜索引擎，显示出协同作用。Epsilon-Q 系统可以成为基于多个光谱库和无标签定量的比较蛋白质组分析的通用工具。
