Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland.
Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.
J Proteome Res. 2021 Jan 1;20(1):776-785. doi: 10.1021/acs.jproteome.0c00651. Epub 2020 Sep 28.
Identification of metal-binding sites in proteins and understanding metal-coupled protein folding mechanisms are aspects of high importance for the structure-to-function relationship. Mass spectrometry (MS) has brought a powerful adjunct perspective to structural biology, obtaining from metal-to-protein stoichiometry to quaternary structure information. Currently, the different experimental and/or instrumental setups usually require the use of multiple data analysis software, and in some cases, they lack some of the main data analysis steps (MS processing, scoring, identification). Here, we present a comprehensive data analysis pipeline that addresses charge-state deconvolution, statistical scoring, and mass assignment for native MS, bottom-up, and native top-down with emphasis on metal-protein complexes. We have evaluated all of the approaches using assemblies of increasing complexity, including free and chemically labeled proteins, from low- to high-resolution MS. In all cases, the results have been compared with common software and proved how MetaOdysseus outperformed them.
鉴定蛋白质中的金属结合位点和理解金属偶联蛋白折叠机制是结构与功能关系的高度重要方面。质谱 (MS) 为结构生物学带来了强大的辅助视角，可获得从金属与蛋白质计量比到四级结构的信息。目前，不同的实验和/或仪器设置通常需要使用多种数据分析软件，并且在某些情况下，它们缺乏一些主要的数据分析步骤（MS 处理、评分、鉴定）。在这里，我们提出了一个全面的数据分析管道，用于解决天然 MS、从头和天然自上而下的电荷态解卷积、统计评分和质量赋值，重点是金属蛋白复合物。我们使用越来越复杂的组装体（包括自由和化学标记的蛋白质），从低分辨率到高分辨率 MS，评估了所有方法。在所有情况下，结果都与常用软件进行了比较，并证明了 MetaOdysseus 如何优于它们。
