德国柏林夏里特医学院Fan Liu等研究人员合作发现，大规模重组标准和稳健的高速搜索引擎可推进交联质谱基础的相互作用组学。2024年10月31日，《自然—方法学》杂志在线发表了这项成果。

研究人员开发了由数百种重组蛋白组成的受控交联质谱（XL-MS）标准，这些蛋白被系统地混合以进行交联。研究人员使用一个标准数据集来指导Scout的开发，Scout是一个用于带有MS可切割交联剂的XL-MS的搜索引擎。通过使用其他独立标准数据集和已发表的数据集，研究人员对Scout和现有XL-MS软件的性能进行了基准测试。结果表明，Scout在速度、灵敏度和假发现率控制方面提供了出色的组合。结果展示了该大规模重组标准如何支持XL-MS分析工具的发展和XL-MS结果的评估。

据悉，推进蛋白质组范围内XL-MS数据分析工具的发展需要模拟生物复杂性的真实标准。

附：英文原文

Title: Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics

Author: Clasen, Milan Avila, Ruwolt, Max, Wang, Cong, Ruta, Julia, Bogdanow, Boris, Kurt, Louise U., Zhang, Zehong, Wang, Shuai, Gozzo, Fabio C., Chen, Tao, Carvalho, Paulo C., Lima, Diogo Borges, Liu, Fan

Issue&Volume: 2024-10-31

Abstract: Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here we develop well-controlled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent standard datasets and published datasets, we benchmark the performance of Scout and existing XL-MS software. We find that Scout offers an excellent combination of speed, sensitivity and false discovery rate control. The results illustrate how our large recombinant standard can support the development of XL-MS analysis tools and evaluation of XL-MS results.

DOI: 10.1038/s41592-024-02478-1

Source: https://www.nature.com/articles/s41592-024-02478-1